Gene

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway

GABAPATHWAY 0.00213 0.017911 0.5 6 12

Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter whose receptor is regulated by Pli

ChemicalGeneticPerturbations

0.001827 0.015951 0.357143 10 28

GILDEA_BLADDER_UP Top 30 genes differentially expressed in metastatic (T24T) and nonmetastatic (T24) human bladder can

CanonicalPathway

DAG (diacylglycerol) signaling activity

SA_DIACYLGLYCEROL_SIGNALING 0.005147 0.0359 0.5 5 10

ChemicalGeneticPerturbations

Downregulated in correlation with incipient Alzheimer's Disease,139 CA1 region of the hippocampu

ALZHEIMERS_INCIPIENT_DN 7.24E-04 0.007805 0.230216 32 in the

na

V$AP3_Q6 TransfacTargets 0.0049 0.034611 0.19598 39 199

TransfacTargets

V$TAL1ALPHAE47_01 na 0.001402 0.013036 0.208333 40 192

TransfacTargets

na

WYAAANNRNNNGCG_UNKNOWN 4.04E-04 0.004942 0.341463 14 41

GOMolecularFunction 0.00213 0.017911

Genes annotated by the GO term

INWARD_RECTIFIER_POTASSIUM_CHANNEL_ACTIVITY GO:0005242. 0.5 6 12

na

V$MIF1_01TransfacTargets 0.002617 0.020908 0.222222 28 126

V$CHOP_01 na

TransfacTargets 0.001141 0.011258 0.211957 39 184

na

V$EGR1_01TransfacTargets 1.01E-05 2.92E-04 0.240196 49 204

microRNATargets

CAATGCA,MIR-33 na 2.90E-04 0.003929 0.269663 24 89

ChemicalGeneticPerturbations follwing VEGF treatment of human myometrial microvascular endothelial cells

VEGF_MMMEC_12HRS_UP 0.00681

Up-regulated at 12hrs 0.04394 0.321429 9 28

na

V$PIT1_Q6 TransfacTargets 1.45E-04 0.002277 0.228261 42 184

ChemicalGeneticPerturbations

0.001563 0.014144 0.208556

AGEING_BRAIN_UP Age-upregulated in the human frontal cortex 39 187

ChemicalGeneticPerturbations

These are 0.001948 0.016684 0.215686 as 153

LI_FETAL_VS_WT_KIDNEY_DN genes identified by simple statistical criteria33 differing in their mRNA expresssion between

GOBiologicalProcess

Genes annotated by the 0.026791 0.314286

0.003503 GO term 11 35

DNA_DAMAGE_RESPONSE__SIGNAL_TRANSDUCTION GO:0042770. A cascade of processes induced by the detection of DN

CanonicalPathway hypertrophy is induced by NF-ATc4 and GATA4, which are49

NFATPATHWAY Cardiac 0.00285 0.022523 0.285714 14 stimulated through calcineurin activ

GenMAPP na

G1_TO_S_CELL_CYCLE_REACTOME 7.97E-07 3.94E-05 0.369231 24 65

ChemicalGeneticPerturbations

BRCA_BRCA1_NEG expression is consistently negatively correlated with brca1 germline status in breast canc

Genes whose5.55E-04 0.006412 0.233577 32 137

microRNATargets

TAGCTTT,MIR-9 na 4.53E-08 3.48E-06 0.270936 55 203

ChemicalGeneticPerturbations cells from elongin-A knockout mice

ELONGINA_KO_UP 2.92E-04 0.003928 0.232258

Upregulated in MES 36 155

V$HNF4_Q6 na

TransfacTargets 0.004101 0.030253 0.19797 39 197

TransfacTargets

TGCTGAY_UNKNOWN na 6.48E-06 2.05E-04 0.205189 87 424

T na

V$MYOD_01ransfacTargets 1.20E-05 3.34E-04 0.242268 47 194

microRNATargets

ATTCTTT,MIR-186 na 0.001726 0.015198 0.199134 46 231

TransfacTargets

GGGAGGRR_V$MAZ_Q6 na 0 0 0.190883 335 1755

T na

V$CEBPA_01ransfacTargets 2.10E-04 0.003071 0.224599 42 187

ChemicalGeneticPerturbations

0.004465 0.032364 0.305556 11 36

ADIP_VS_PREADIP_DN Downregulated in mature murine adipocytes (7 day differentiation) vs. preadipocytes (6 hr differentia

GOBiologicalProcess

Genes 0.004899 GO term 0.240506 19 79

GENERATION_OF_NEURONS annotated by the 0.034704 GO:0048699. The process by which nerve cells are generated. This in

TransfacTargets

RRAGTTGT_UNKNOWNna 5.26E-04 0.006157 0.218579 40 183

V$SMAD4_Q6 na

TransfacTargets 7.34E-04 0.007888 0.216667 39 180

GOMolecularFunction 6.19E-04 0.006935 0.298246

Genes annotated by the GO 17 57

STRUCTURAL_CONSTITUENT_OF_CYTOSKELETON term GO:0005200. The action of a molecule that contributes to the struct

ChemicalGeneticPerturbations left ventricle myocardium of patients with heart failure following implantation o

LVAD_HEARTFAILURE_DN 4.71E-04

Downregulated in the 0.005605 0.351351 13 37

microRNATargets

TGAGATT,MIR-216 na 0.001207 0.011657 0.25 23 92

microRNATargets

GCAAAAA,MIR-129 na 1.25E-07 8.69E-06 0.283951 46 162

GNF2_CENPF na

CancerGeneNeighborhood 2.05E-06 8.32E-05 0.381818 21 55

GNF2_CENPE na

CancerGeneNeighborhood 1.16E-04 0.001925 0.378378 14 37

TransfacTargets

na

V$CACBINDINGPROTEIN_Q6 1.52E-05 4.07E-04 0.24581 44 179

ChemicalGeneticPerturbations

Down-regulated

0.007289 0.045558 0.368421 7 19

CMV_HCMV_TIMECOURSE_18HRS_DN in fibroblasts following infection with human cytomegalovirus (at least 3-fold, with Af

ChemicalGeneticPerturbations pediatric acute myeloid leukemia (AML) subtype t(15;17)[PML-RAR-alpha].

ROSS_PML_RAR 0.006216

Genes that distinguish 0.040682 0.24 18 75

TransfacTargets

GGGCGGR_V$SP1_Q6 na 1.61E-08 1.34E-06 0.16773 368 2194

V$NKX3A_01 na

TransfacTargets 0.001264 0.012068 0.215569 36 167

TransfacTargets

V$CREBP1_Q2 na 0.001141 0.011258 0.211957 39 184

ChemicalGeneticPerturbations

Genes selected in supervised analyses to discriminate cells expressing E2F3 oncogene from control cel

E2F3_ONCOGENIC_SIGNATURE 8.57E-07 4.19E-05 0.247788 56 226

TransfacTargets

TTCYRGAA_UNKNOWNna 0.005492 0.037319 0.189655 44 232

na

V$OSF2_Q6TransfacTargets 2.49E-04 0.003521 0.218447 45 206

na

V$ZF5_01 TransfacTargets 1.63E-05 4.24E-04 0.243243 45 185

ChemicalGeneticPerturbations

Up-regulated0.002286 0.01887

at 4 0.4 8 20

BLEO_HUMAN_LYMPH_HIGH_4HRS_UP hours following treatment of human lymphocytes (TK6) with a high dose of bleomyc

TransfacTargets

na

YNTTTNNNANGCARM_UNKNOWN 1.44E-06 6.32E-05 0.388889 21 54

C na

module_390 ancerModules 0.007037 0.044824 0.571429 4 7

na

V$IRF7_01 TransfacTargets 0.004783 0.033929 0.195122 40 205

CanonicalPathway and 0.008179 0.049209 while cdk2/cyclin E promotes the G1/S transition.

SA_G1_AND_S_PHASES Cdk2, 4, 6 bind cyclin D in G1, 0.4 6 15

ChemicalGeneticPerturbationssodium arsenite in fibroblasts (Clusters 4, 5, and 6)

AS3_FIBRO_DN 2.76E-04 0.003826 0.387097

Downregulated by 12 31

TransfacTargets

YYCATTCAWW_UNKNOWN na 0.004175 0.030615 0.209459 31 148

ChemicalGeneticPerturbations human granulosa cells by the gonadotropins LH and FSH, as well as by cAMP-stimu

GN_CAMP_GRANULOSA_DN 0.006857 0.043958 0.254237

Down-regulated in 15 59

GOBiologicalProcess

Genes annotated by

0.003738 GO term 0.20915 32

REGULATION_OF_TRANSFERASE_ACTIVITY the 0.028031 GO:0051338. Any process that153 modulates the frequency, rate or ext

TransfacTargets

TGAYRTCA_V$ATF3_Q6 na 1.25E-07 8.58E-06 0.221411 91 411

ChemicalGeneticPerturbationsstable, ectopic 0.211921

Up-regulated with 32 151

BRCA1_OVEREXP_PROSTATE_UP 0.003022 0.023395 overexpression of BRCA1 in DU-145 human prostate cancer cell lines

CMV_ALL_DN Downregulated at any 0.017137 0.237624

0.002018

ChemicalGeneticPerturbations timepoint following infection of24 101

primary human foreskin fibroblasts with CMV

GOBiologicalProcess

Genes 9.05E-04 GO term 0.193443 59 305

CELL_CYCLE_GO_0007049 annotated by the 0.009416 GO:0007049. The progression of biochemical and morphological pha

na

V$ARP1_01TransfacTargets 5.03E-04 0.005895 0.24 30 125

CK1PATHWAY Caseine 3.77E-04 0.004727 0.5 8 16

CanonicalPathway kinase 1 (CK1) and cdk5 phosphorylate DARPP32 in the dopamine signaling pathway.

C na

module_381 ancerModules 1.51E-06 6.55E-05 0.75 9 12

C na

module_382 ancerModules 0.00681 0.04394 0.321429 9 28

GOCellularComponent 0.005388 0.03691 0.276596

Genes annotated 13 47

MICROTUBULE_ASSOCIATED_COMPLEX by the GO term GO:0005875. Any multimeric complex connected to a microtubule.

ChemicalGeneticPerturbations glomeruli of cadaver kidneys from patients with diabetic nephropathy, compare

DIAB_NEPH_DN 3.20E-04 0.00419 0.195335

Downregulated in the 67 343

TransfacTargets

V$E2F_Q6_01 na 2.83E-04 0.003873 0.226744 39 172

ChemicalGeneticPerturbations

IRITANI_ADPROX_LYMPH 1

LYMPHATIC EC.82E-05 4.55E-04 0.272727 33 121

na

V$CIZ_01 TransfacTargets 2.90E-04 0.00395 0.224719 40 178

na

V$TST1_01 TransfacTargets 0.001538 0.014044 0.20603 41 199

ChemicalGeneticPerturbations

IRS_KO_ADIP_DN down-regulated in brown preadipocytes 11 four Irs-knockout mouse lines with increas

Progressively0.004465 0.032364 0.305556 from 36

KEGG na

HSA05110_CHOLERA_INFECTION 4.04E-04 0.004942 0.341463 14 41

ChemicalGeneticPerturbations

IDX_TSA_DN_CLUSTER3 0.005356 0.036744 0.243243 18 74

Strongly down-regulated at 8-96 hours during differentiation of 3T3-L1 fibroblasts into adipocytes with

ChemicalGeneticPerturbations

Down-regulated in

6.32E-07 3.22E-05 0.45 18 any

AGED_MOUSE_HIPPOCAMPUS_ANY_DN the hippocampus of 16-month aged mice from40 of four strains (S8, S10, SR1, B6

ChemicalGeneticPerturbations

Cell-cycle 5.80E-04 0.006626 0.238095 30 126

SERUM_FIBROBLAST_CELLCYCLE dependent genes regulated following exposure to serum in a variety of human fibroblast cel

ChemicalGeneticPerturbations

IDX_TSA_DN_CLUSTER2 down-regulated from 8-96 hours 20 62

Progressively 6.32E-05 0.001192 0.322581 during differentiation of 3T3-L1 fibroblasts into adipocy

GOMolecularFunction

Genes annotated by the 2.68E-04 0.55 11 20

GLUTAMATE_RECEPTOR_ACTIVITY 8.97E-06 GO term GO:0008066. Combining with glutamate to initiate a change in cell a

ChemicalGeneticPerturbations 48-96 hours during differentiation of 3T3-L1 fibroblasts into adipocytes with IDX (in

IDX_TSA_DN_CLUSTER1 0.00449 0.032403 0.292683

Down-regulated at 12 41

na

V$AP4_01 TransfacTargets 0.004101 0.030253 0.19797 39 197

ChemicalGeneticPerturbations

CMV_IE86_UP by expression of cytomegalovirus IE86 protein in primary human fibroblasts

Upregulated 0.001189 0.011578 0.3 15 50

na

V$ZIC2_01 TransfacTargets 5.46E-05 0.001065 0.234043 44 188

ChemicalGeneticPerturbations

Up-regulated in fibroblasts following infection 82 439

CMV_HCMV_TIMECOURSE_ALL_UP 3.36E-04 0.004334 0.186788 with human cytomegalovirus (at least 3-fold, with Affym

na

V$HSF1_01TransfacTargets 0.001391 0.013013 0.207071 41 198

ChemicalGeneticPerturbations

ALZHEIMERS_DISEASE_UP in correlation with overt Alzheimer's Disease, in the CA1 region of the hippocampus

Upregulated 0.007549 0.046543 0.151012 209 1384

TransfacTargets

TGCCAAR_V$NF1_Q6 na 2.91E-05 6.61E-04 0.190654 102 535

GOBiologicalProcess

Genes annotated by the 0.049209 GO:0008630. A cascade of processes initiated by the detection of DN

0.008179 GO term 0.4

DNA_DAMAGE_RESPONSE__SIGNAL_TRANSDUCTION_RESULTING_IN_INDUCTION_OF_APOPTOSIS 6 15

microRNATargets

TAATAAT,MIR-126 na 6.61E-04 0.007287 0.216216 40 185

TransfacTargets

CTTTAAR_UNKNOWN na 2.59E-05 6.00E-04 0.180723 135 747

GOCellularComponent 0.008097 GO term 0.209677 26 124

ACTIN_CYTOSKELETONGenes annotated by the 0.049134 GO:0015629. The part of the cytoskeleton (the internal framework o

ChemicalGeneticPerturbations

Down-regulated

0.001599 0.014334 0.238095

CMV_HCMV_TIMECOURSE_48HRS_DN in fibroblasts following infection with 25 105

human cytomegalovirus (at least 3-fold, with Af

microRNATargets

na 1.13E-08 9.53E-07 0.218504

GCACTTT,MIR-17-5P,MIR-20A,MIR-106A,MIR-106B,MIR-20B,MIR-519D 111 508

GenMAPP na

SMOOTH_MUSCLE_CONTRACTION 2.90E-06 1.06E-04 0.280303 37 132

GOCellularComponent 0.005147 GO term GO:0030426. The migrating motile tip of a growing nerve cell axon o

GROWTH_CONE Genes annotated by the 0.0359 0.5 5 10

GOCellularComponent 4.33E-04 GO term 0.209607 48 229

CYTOSKELETAL_PART Genes annotated by the 0.005232 GO:0044430. Any constituent part of the cytoskeleton, a cellular sca

TransfacTargets

GGCKCATGS_UNKNOWN na 0.00185 0.016009 0.297872 14 47

TransfacTargets

AAAYWAACM_V$HFH4_01 na 1.25E-04 0.002037 0.223301 46 206

C na

GCM_PTPRDancerGeneNeighborhood 0.002269 0.018759 0.283019 15 53

ChemicalGeneticPerturbations

0.002413 0.019528 0.241758 22 91

MANALO_HYPOXIA_UPGenes upregulated in human pulmonary endothelial cells under hypoxic conditions or after exposure t

na

V$LYF1_01 TransfacTargets 1.75E-04 0.002679 0.221675 45 203

ChemicalGeneticPerturbations genes in KCL22 cells

TAVOR_CEBP_UP 9.44E-04 0.009678 0.306122

C/EBP up-regulated 15 49

na

V$OCT1_B TransfacTargets 6.67E-04 0.007335 0.211823 43 203

CanonicalPathway functions as a second messenger activating the9

CACAMPATHWAY Calcium 1.51E-06 6.55E-05 0.75 12

calcium/calmodulin-dependent kinases, which

GOBiologicalProcess 0.004634 GO term 0.208054 31 149

MITOTIC_CELL_CYCLE Genes annotated by the 0.033062 GO:0000278. Progression through the phases of the mitotic cell cycl

ChemicalGeneticPerturbations

HALMOS_CEBP_UP top upregulated genes based on 15 49

The list of the9.44E-04 0.009678 0.306122 an analysis comparing 0 versus 6 h of C/EBP induction

na

V$HFH8_01TransfacTargets 2.49E-04 0.003519 0.22807 39 171

GCM_MAPK10 na

CancerGeneNeighborhood 0 0 0.435897 34 78

na

V$VDR_Q3 TransfacTargets 9.14E-04 0.009486 0.215909 38 176

T na

V$STAT3_02 ransfacTargets 0.008129 0.049209 0.214286 24 112

na

V$SOX5_01TransfacTargets 0.007091 0.044881 0.192893 38 197

TransfacTargets

V$TAXCREB_01 na 0.008095 0.049179 0.216981 23 106

microRNATargets

CATTTCA,MIR-203 na 1.21E-04 0.001988 0.214575 53 247

ChemicalGeneticPerturbations vastus lateralis muscle of aged vs. young adult rhesus monkeys

AGED_RHESUS_UP in the

Upregulated 0.002874 0.022642 0.203209 38 187

ChemicalGeneticPerturbations desmoplastic medulloblastomas. (p 1.4, mean average difference

ASTON_DEPRESSION_UP 0.003591 0.02717

Genes upregulated 0.3 12 40

microRNATargets

TGCTTTG,MIR-330 na 7.58E-09 6.64E-07 0.254417 72 283

TransfacTargets

YTAAYNGCT_UNKNOWN na 0.0065 0.042214 0.215517 25 116

TransfacTargets

TCCATTKW_UNKNOWN na 4.16E-05 8.62E-04 0.236559 44 186

TransfacTargets

GGGTGGRR_V$PAX4_03 na 1.18E-10 1.47E-08 0.197225 199 1009

na

V$ZIC3_01 TransfacTargets 2.53E-05 5.92E-04 0.234146 48 205

microRNATargets

TTTGTAG,MIR-520D na 3.68E-07 2.07E-05 0.236934 68 287

na

V$NFY_01 TransfacTargets 0.008147 0.049199 0.193548 36 186

na

V$P53_02 TransfacTargets 2.65E-06 9.93E-05 0.251282 49 195

na

V$WHN_B TransfacTargets 0.008147 0.049199 0.193548 36 186

ChemicalGeneticPerturbations

Effect of 1.48E-04 on gene transcription 39

TAKEDA_NUP8_HOXA9_3D_UP NUP98-HOXA9 0.002315 0.233533 at 3 d after transduction UP 167

T na

V$E4BP4_01ransfacTargets 1.85E-04 0.00279 0.233129 38 163

TransfacTargets

TGACCTY_V$ERR1_Q2 na 2.90E-07 1.68E-05 0.190594 154 808

ChemicalGeneticPerturbations

0.006178 0.040492 0.264151 14

JECHLINGER_EMT_UP Genes upregulated for epithelial plasticity in tumor progression 53

GOMolecularFunction 1.48E-07 GO term GO:0022891.

Genes annotated by the 9.61E-06 0.231454 78 337

SUBSTRATE_SPECIFIC_TRANSMEMBRANE_TRANSPORTER_ACTIVITY Catalysis of the transfer of a specific substance or grou

VIPPATHWAY Apoptosis 8.11E-05 cells is inhibited by vasoactive11

CanonicalPathway of activated T 0.001462 0.458333 24

intestinal peptide (VIP) and its relative PACAP.

GOBiologicalProcess

Genes 1.68E-11 2.46E-09 0.394118 67 170

SYNAPTIC_TRANSMISSION annotated by the GO term GO:0007268. The process of communication from a neuron to a targ

NO1PATHWAY Shear stress in endothelial cells increases0.36

CanonicalPathway 0.002886 0.022555 9 25

cytoplasmic calcium, which activates nitric oxide synthase III

na

V$HEN1_02TransfacTargets 0.005742 0.038391 0.206897 30 145

TransfacTargets

na

RYCACNNRNNRNCAG_UNKNOWN 9.00E-05 0.001571 0.333333 18 54

na

V$LFA1_Q6TransfacTargets 2.38E-04 0.00338 0.223404 42 188

microRNATargets

GCTTGAA,MIR-498 na 0.005644 0.037835 0.223301 23 103

ChemicalGeneticPerturbations in 0.004467 cells.

CHIARETTI_T_ALL 3.49E-04

Genes overexpressed leukemia 0.209205 50 239

CanonicalPathwayPlk3 phosphorylates CDC25c,0.571429 the G2/M 4

PLK3PATHWAY Active 0.007037 0.044824 blocking 7

transition, and phosphorylates p53 to induce a

TransfacTargets

V$AP2_Q6_01 na 0.005127 0.035959 0.197861 37 187

TransfacTargets

SMTTTTGT_UNKNOWNna 3.14E-04 0.004133 0.197531 64 324

TransfacTargets

RYTGCNWTGGNR_UNKNOWN na 0.001104 0.011001 0.255814 22 86

GOBiologicalProcess

Genes annotated

0.002198 GO term 0.188552 56

REGULATION_OF_CELL_PROLIFERATION by the 0.018292 GO:0042127. Any process that297 modulates the frequency, rate or ext

ChemicalGeneticPerturbations in control vs bmyb morpholino knockdown in161 fish

Genes upregulated

SHEPARD_BMYB_MORPHOLINO_DN 0.002429 0.01963 0.21118 34 zebra

CanonicalPathway erythropoietin (Epo) 0.545455 6 11

EPONFKBPATHWAY The cytokine0.001196 0.011594 prevents stress-induced neuronal apoptosis by stimulating anti-apop

GOBiologicalProcess

Genes annotated by the GO term 0.222973

0.001085 33 148

SECOND_MESSENGER_MEDIATED_SIGNALING 0.010836 GO:0019932. A series of molecular signals in which an ion or small m

na

V$EGR3_01TransfacTargets 0.001175 0.011465 0.283333 17 60

CanonicalPathwayactivates the cdc2/cyclin B complex to induce the G2/M transition.

SA_G2_AND_M_PHASES Cdc25 0.001432 0.013216 0.625 5 8

na

V$GRE_C TransfacTargets 1.75E-04 0.002683 0.264706 27 102

microRNATargets

na 4.11E-07 2.23E-05 0.206107

TGCTGCT,MIR-15A,MIR-16,MIR-15B,MIR-195,MIR-424,MIR-497 108 524

V$FOXM1_01 na

TransfacTargets 0.005015 0.035323 0.196891 38 193

ChemicalGeneticPerturbations nucleus accumbens of mice after 2 weeks of induction of transgenic deltaFosB

DFOSB_BRAIN_2WKS_UP in the

Up-regulated 8.15E-05 0.001459 0.388889 14 36

GOBiologicalProcess

Genes annotated by the 0.015951 GO:0003001.

0.001827 GO term 0.357143 10 28

GENERATION_OF_A_SIGNAL_INVOLVED_IN_CELL_CELL_SIGNALING The cellular process by which a physical entity or chan

C na

module_540 ancerModules 6.10E-04 0.006848 0.6 6 10

GOBiologicalProcess

Genes annotated by the GO term

0.00235 0.4375

MITOTIC_SISTER_CHROMATID_SEGREGATION 0.019177 GO:0000070. The cell 7 16

cycle process whereby replicated homologous

GOBiologicalProcess

Genes annotated by the GO term GO:0006813. The directed movement of potassium ions (K+) into, ou

POTASSIUM_ION_TRANSPORT 2.12E-05 5.14E-04 0.344828 20 58

C na

module_334 ancerModules 7.52E-05 0.001366 0.245033 37 151

GOMolecularFunction 6.13E-09 5.57E-07 0.333333

Genes 40 120

GATED_CHANNEL_ACTIVITY annotated by the GO term GO:0022836. Catalysis of the transmembrane transfer of a solute by

C na

module_342 ancerModules 0.005346 0.036776 0.195 39 200

TransfacTargets

V$PTF1BETA_Q6 na 2.58E-06 9.78E-05 0.255435 47 184

C na

module_533 ancerModules 1.61E-08 1.32E-06 0.5 20 40

CancerGeneNeighborhood

GNF2_TM4SF2 na 0 0 0.909091 20 22

ChemicalGeneticPerturbations

0.007789 0.047788 0.75 3

CHEOK_HDMTX_UP Genes upregulated by high-dose methotrexate (HDMTX) treatment4(P 1.4, mean average differen

C na

module_241 ancerModules 5.97E-04 0.006772 0.277778 20 72

KEGG na

HSA05219_BLADDER_CANCER 0.00449 0.032403 0.292683 12 41

na

V$HLF_01 TransfacTargets 2.26E-06 8.82E-05 0.252577 49 194

GOMolecularFunction 0.007184 0.045182 GO:0003779. Interacting selectively with monomeric or multimeric f

ACTIN_BINDING Genes annotated by the GO term 0.236842 18 76

T na

V$NMYC_01 ransfacTargets 0.002999 0.023293 0.199029 41 206

ChemicalGeneticPerturbations

RUIZ_TENASCIN_TARGETS 3.71E-05

Tenascin-C target genes 7.96E-04 0.303797 24 79

C na

module_451 ancerModules 0.004291 0.031329 0.322581 10 31

TransfacTargets

V$E2F1DP2_01 na 0.007178 0.045375 0.197674 34 172

GOMolecularFunction 0.001207 0.011657 GO:0003924. Catalysis of the reaction: GTP + H2O = GDP + phosphat

GTPASE_ACTIVITY Genes annotated by the GO term 0.25 23 92

KEGG na 2.78E-04 0.00385

HSA00471_D_GLUTAMINE_AND_D_GLUTAMATE_METABOLISM 1 4 4

ChemicalGeneticPerturbations

BRCA_ER_NEG expression is consistently negatively correlated with estrogen receptor status in breast c

Genes whose5.20E-07 2.70E-05 0.186364 164 880

GOMolecularFunction 8.92E-04 GO term

Genes annotated by the 0.00932 0.5 7 14

CYCLIC_NUCLEOTIDE_PHOSPHODIESTERASE_ACTIVITY GO:0004112. Catalysis of the reaction: a nucleoside cyclic phosphate

ChemicalGeneticPerturbations

The 50 most significantly down-regulated genes in MM in comparison with normal bone marrow PCs

3.01E-04

ZHAN_MULTIPLE_MYELOMA_VS_NORMAL_DN0.004025 0.35 14 40

microRNATargets

GTGGTGA,MIR-197 na 0.004555 0.03278 0.258065 16 62

GNF2_PCNA na

CancerGeneNeighborhood 1.22E-06 5.66E-05 0.370968 23 62

ChemicalGeneticPerturbations

HSC_HSC_FETAL in mouse 0.047069 0.18894 fetal (HSC

Up-regulated0.007644 hematopoietic stem cells from 41 liver 217 Shared + Fetal)

KEGG na

HSA04730_LONG_TERM_DEPRESSION 3.20E-04 0.004197 0.283784 21 74

KEGG na

HSA04510_FOCAL_ADHESION 3.39E-04 0.004368 0.219895 42 191

microRNATargets

na

AAAGGGA,MIR-204,MIR-211 7.38E-05 0.001355 0.229592 45 196

GOBiologicalProcess

Genes annotated by the GO term GO:0007215. The series of molecular signals generated as a consequ

GLUTAMATE_SIGNALING_PATHWAY 0.003553 0.02705 0.411765 7 17

GOMolecularFunction 0.001321 GO term 0.194245

Genes 54 278

PROTEIN_KINASE_ACTIVITY annotated by the 0.012472 GO:0004672. Catalysis of the phosphorylation of an amino acid resid

TransfacTargets

V$TCF11MAFG_01 na 0.003678 0.027707 0.206061 34 165

C na

module_214 ancerModules 5.59E-05 0.001086 0.444444 12 27

C na

module_215 ancerModules 2.06E-06 8.24E-05 0.666667 10 15

microRNATargets

TGCCTTA,MIR-124A na 9.49E-09 8.18E-07 0.221532 107 483

ChemicalGeneticPerturbations mouse aorta by chronic treatment with PPARgamma agonist rosiglitazone

ROS_MOUSE_AORTA_DN 0.002233 0.018495 0.256757

Down-regulated in 19 74

ChemicalGeneticPerturbations

CMV-UV_HCMV_6HRS_UP in fibroblasts at 6 hours following 30 114

Up-regulated 8.83E-05 0.001553 0.263158 infection with UV-inactivated human cytomegalovirus

KEGG

HSA04110_CELL_CYCLEna 3.77E-04 0.00472 0.25 28 112

na

V$CEBP_Q2TransfacTargets 0.002665 0.02116 0.206897 36 174

TransfacTargets

V$AP1_Q4_01 na 3.12E-04 0.004136 0.216346 45 208

CanonicalPathway of Neurotransmitter Relase by Botulinum Toxin

BOTULINPATHWAY Blockade 0.001248 0.011962 0.8 4 5

CancerGeneNeighborhood

GNF2_SMC4L1 na 7.07E-06 2.19E-04 0.324675 25 77

microRNATargets

CTTGTAT,MIR-381 na 5.76E-04 0.006615 0.22093 38 172

C na

module_220 ancerModules 0.007754 0.04763 0.176829 58 328

microRNATargets

GTACAGG,MIR-486 na 9.44E-04 0.009678 0.306122 15 49

TransfacTargets

GGGYGTGNY_UNKNOWN na 4.91E-06 1.62E-04 0.2 99 495

TransfacTargets

YNGTTNNNATT_UNKNOWN na 2.99E-09 3.04E-07 0.261029 71 272

microRNATargets

na

TTGCACT,MIR-130A,MIR-301,MIR-130B 1.30E-04 0.002095 0.20059 68 339

microRNATargets

ATGCTGG,MIR-338 na 0.00151 0.013814 0.242424 24 99

V$FOXJ2_01 na

TransfacTargets 0.001739 0.015288 0.217105 33 152

GenMAPP na

CELL_CYCLE_KEGG 4.72E-05 9.50E-04 0.294118 25 85

KEGG na 0.007289 0.045558 0.368421

HSA05030_AMYOTROPHIC_LATERAL_SCLEROSIS 7 19

TransfacTargets

GATAAGR_V$GATA_C na 0.005327 0.036695 0.189076 45 238

na

V$EGR2_01TransfacTargets 4.53E-10 5.03E-08 0.322368 49 152

na

V$PR_Q2 TransfacTargets 1.35E-04 0.002144 0.225641 44 195

C na

module_426 ancerModules 9.33E-04 0.00965 0.258824 22 85

microRNATargets

CTTTGCA,MIR-527 na 3.31E-05 7.34E-04 0.231884 48 207

GOBiologicalProcess

Genes annotated by the 0.037331 GO:0045055. The regulated secretory pathway is a second secretory

REGULATED_SECRETORY_PATHWAY 0.005502 GO term 0.428571 6 14

na

V$HSF2_01TransfacTargets 1.86E-04 0.002788 0.225806 42 186

CancerGeneNeighborhood

GNF2_SMC2L1 na 6.66E-06 2.08E-04 0.466667 14 30

microRNATargets

TGCAAAC,MIR-452 na 0.002078 0.017619 0.244444 22 90

TransfacTargets

YGCANTGCR_UNKNOWN na 3.30E-04 0.004272 0.263158 25 95

TransfacTargets

V$CDPCR3HD_01 na 1.30E-05 3.58E-04 0.243386 46 189

TransfacTargets

TATAAA_V$TATA_01 na 4.11E-06 1.42E-04 0.177958 176 989

GOBiologicalProcess

Genes annotated by the 0.04394 0.321429 9 28

RESPONSE_TO_NUTRIENT_LEVELS 0.00681 GO term GO:0031667. A change in state or activity of a cell or an organism (in

TransfacTargets

CGTSACG_V$PAX3_B na 2.09E-04 0.003054 0.262136 27 103

C na

module_485 ancerModules 4.47E-04 0.005364 0.326087 15 46

GOBiologicalProcess

Genes annotated by the GO term GO:0008629.

0.008308 0.04975 8 24

INDUCTION_OF_APOPTOSIS_BY_INTRACELLULAR_SIGNALS0.333333 Any process induced by intracellular signals that direct

KEGG na

HSA04912_GNRH_SIGNALING_PATHWAY 6.92E-04 0.007531 0.255319 24 94

GOMolecularFunction 1.84E-07 GO

Genes annotated by the 1.14E-05 0.666667 12 18

VOLTAGE_GATED_CALCIUM_CHANNEL_ACTIVITY term GO:0005245. Catalysis of the transmembrane transfer of a calcium i

KEGG na

HSA04740_OLFACTORY_TRANSDUCTION 1.30E-04 0.002089 0.413793 12 29

GOBiologicalProcess

Genes annotated by

8.82E-04 GO term 0.192926 60

REGULATION_OF_MOLECULAR_FUNCTION the 0.009231 GO:0065009. Any process that311 modulates the frequency, rate or ext

ChemicalGeneticPerturbations

4.04E-04 0.004942 0.341463 14 41

PASSERINI_APOPTOSIS Genes associated with cellular adhesion that are differentially expressed in endothelial cells of pig aort

CanonicalPathway a benzodiazepine receptor antagonist that5may induce protective preconditioning in isch

FLUMAZENILPATHWAYFlumazenil is0.002879 0.022604 0.555556 9

ChemicalGeneticPerturbations

Up-regulated0.007895 0.048256 0.239437

in 17 71

CMV_HCMV_TIMECOURSE_24HRS_UP fibroblasts following infection with human cytomegalovirus (at least 3-fold, with Affym

TransfacTargets

CTGCAGY_UNKNOWN na 0 0 0.244406 142 581

TransfacTargets

AAAYRNCTG_UNKNOWN na 0.007235 0.045335 0.180272 53 294

TransfacTargets

V$SP1_Q2_01 na 5.32E-04 0.006202 0.216931 41 189

TransfacTargets

YCATTAA_UNKNOWN na 1.97E-04 0.002924 0.189815 82 432

GOBiologicalProcess 0 0 0.258794 103

CELL_CELL_SIGNALING Genes annotated by the GO term GO:0007267. Any process that398 mediates the transfer of information

C na

module_205 ancerModules 0.008093 0.049231 0.181159 50 276

microRNATargets

na

AATGTGA,MIR-23A,MIR-23B 2.90E-04 0.00396 0.19346 71 367

C na

module_497 ancerModules 6.06E-04 0.006819 0.37931 11 29

na

V$CRX_Q4 TransfacTargets 4.33E-04 0.005212 0.214634 44 205

V$HOX13_01 na

TransfacTargets 0.005531 0.037324 0.3125 10 32

GOMolecularFunction 0.002877 0.022623 0.197248

Genes annotated by the GO term 43 218

HYDROLASE_ACTIVITY__ACTING_ON_ACID_ANHYDRIDESGO:0016817. Catalysis of the hydrolysis of any acid anhydride.

na

V$EFC_Q6 TransfacTargets 2.79E-04 0.003848 0.217391 45 207

na

V$MYB_Q6TransfacTargets 0.001141 0.011258 0.211957 39 184

na

GCM_PTK2 CancerGeneNeighborhood 7.97E-04 0.008446 0.231343 31 134

na

V$MYB_Q3TransfacTargets 0.001271 0.012109 0.212291 38 179

KEGG na 1.02E-05 2.91E-04 0.231092

HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION 55 238

TransfacTargets

TGACAGNY_V$MEIS1_01 na 2.64E-05 6.08E-04 0.185714 117 630

na

V$HFH1_01TransfacTargets 0.003112 0.023948 0.201031 39 194

ChemicalGeneticPerturbations the nucleus accumbens of mice after 8 weeks of induction of transgenic CREB

CREB_BRAIN_8WKS_DN 2.58E-04 0.003622 0.340909

Down-regulated in 15 44

TransfacTargets

ARGGGTTAA_UNKNOWN na 0.00293 0.022795 0.234694 23 98

TransfacTargets

TGANTCA_V$AP1_C na 4.88E-09 4.60E-07 0.197022 172 873

TransfacTargets

V$TAL1BETAITF2_01 na 0.001717 0.015173 0.206186 40 194

ChemicalGeneticPerturbations by Wnt in HC110.297872 epithelial cells) 47

KENNY_WNT_UP 0.00185 0.016009 (mammary

Genes up-regulated 14

GOCellularComponent 4.34E-06 GO term GO:0044456. The junction between a nerve fiber of one neuron and

SYNAPSE_PART Genes annotated by the 1.47E-04 0.692308 9 13

TransfacTargets

TGACCTTG_V$SF1_Q6 na 9.44E-07 4.58E-05 0.257732 50 194

GOMolecularFunction 1.87E-07 GO

Genes annotated by the 1.14E-05 0.243542 66 271

ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY term GO:0015075. Catalysis of the transfer of an ion from one side of a m

GOBiologicalProcess

Genes annotated by the 0.012176 GO:0007186.

0.00128 GO term 0.189441 61 322

G_PROTEIN_COUPLED_RECEPTOR_PROTEIN_SIGNALING_PATHWAY The series of molecular signals generated as a consequ

ChemicalGeneticPerturbations

Sixty-nine genes commonly upregulated in undifferentiated cancer relative to well-differentiated canc

CANCER_UNDIFFERENTIATED_META_UP 0.001385 0.012998 0.272727 18 66

TransfacTargets

CATTGTYY_V$SOX9_B1na 5.76E-04 0.006601 0.199288 56 281

GOMolecularFunction

Genes annotated by the GO term 0.34 17 50

POTASSIUM_CHANNEL_ACTIVITY 1.06E-04 0.001796 GO:0005267. Catalysis of facilitated diffusion of a potassium ion (by

na

GNF2_MSNCancerGeneNeighborhood 0.006233 0.040691 0.347826 8 23

CanonicalPathway Rho coordinate to induce cyclin 8 22

RACCYCDPATHWAY Ras, Rac, and0.004576 0.03274 0.363636 D1 expression and activate cdk2 to promote the G1/S tra

na

V$AP1_C TransfacTargets 4.33E-04 0.005232 0.209607 48 229

V$HNF6_Q6 na

TransfacTargets 2.51E-05 5.91E-04 0.239362 45 188

ChemicalGeneticPerturbations

Effect of 0.00215 on gene transcription 31

TAKEDA_NUP8_HOXA9_8D_UP NUP98-HOXA9 0.017953 0.21831 at 8 d after transduction UP 142

ChemicalGeneticPerturbations at 3.55E-04 0.303371

IDX_TSA_UP_CLUSTER3 1.28E-05 27 89

Strongly up-regulated 16-24 hours during differentiation of 3T3-L1 fibroblasts into adipocytes with I

GOBiologicalProcess

Genes annotated by the 0.004223 GO:0007188. The series of molecular signals generated as a consequ

3.24E-04 GO term 0.296875

G_PROTEIN_SIGNALING__COUPLED_TO_CAMP_NUCLEOTIDE_SECOND_MESSENGER 19 64

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GOMolecularFunction 0.015374 0.047402 GO:0048487. Interacting selectively with the microtubule constituen

BETA_TUBULIN_BINDING Genes annotated by the GO term 0.1 1 10

ChemicalGeneticPerturbations

6.40E-11 2.25E-09 0.189189 of 37

ADIP_DIFF_CLUSTER5 Strongly upregulated at 24 hours during differentiation 7 3T3-L1 fibroblasts into adipocytes (cluster 5

GNF2_CDC2 na

CancerGeneNeighborhood 7.09E-11 2.15E-09 0.127273 7 55

CanonicalPathway

PTC1PATHWAY 0.015374 0.047402 0.1 1 10

The binding of extracellular signaling protein Sonic hedgehog to the Patched receptor (Ptc1) allows pro

YU_CMYC_UP Myc-activated genes

1.67E-09 3.18E-08 0.147059

ChemicalGeneticPerturbations 5 34

ChemicalGeneticPerturbations

Genes 3.99E-08 multiple 0.173913 4 23

CROONQUIST_IL6_RAS_DN dowmregulated in5.11E-07 myeloma cells exposed to the pro-proliferative cytokine IL-6 versus

GNF2_CCNB2 na

CancerGeneNeighborhood 1.91E-10 4.90E-09 0.115385 6 52

C na

GNF2_MSH2ancerGeneNeighborhood 8.43E-06 6.38E-05 0.115385 3 26

C na

GNF2_ESPL1 ancerGeneNeighborhood 4.40E-11 2.93E-09 0.2 7 35

ChemicalGeneticPerturbations

2.28E-09 timepoints (4-8 hrs) 4 12

P21_P53_EARLY_DN Down-regulated at early 4.10E-08 0.333333 following ectopic expression of p21 (CDKN1A) in OvCa ce

GNF2_MCM4 na

CancerGeneNeighborhood 5.82E-11 2.42E-09 0.2 10 50

GNF2_MKI67 na

CancerGeneNeighborhood 4.37E-10 9.70E-09 0.192308 5 26

C na

module_451 ancerModules 1.40E-07 1.58E-06 0.129032 4 31

C na

module_283 ancerModules 0.010786 0.03487 0.142857 1 7

CanonicalPathway

CDC25PATHWAY 0.013847 0.043295 0.111111 1 9

The protein phosphatase Cdc25 is phosphorylated by Chk1 and activates Cdc2 to stimulate eukaryotic

C na

module_403 ancerModules 1.04E-10 3.02E-09 0.130435 6 46

ChemicalGeneticPerturbationsDAC treatment in LD419 fibroblast cells

DAC_FIBRO_DN 1.03E-04 6.48E-04

Downregulated by 0.2 2 10

na

GNF2_TTK CancerGeneNeighborhood 2.33E-07 2.42E-06 0.114286 4 35

GNF2_CCNA2 na

CancerGeneNeighborhood 4.93E-11 2.98E-09 0.16129 10 62

ChemicalGeneticPerturbations

5.76E-06 4.62E-05 0.130435

P21_P53_MIDDLE_DN Down-regulated at intermediate timepoints (12-16 hrs) 3 ectopic expression of p21 (CDKN1A)

following 23

GNF2_HMMR na

CancerGeneNeighborhood 5.77E-11 2.74E-09 0.159091 7 44

ChemicalGeneticPerturbations

Putative 1.96E-09 3.62E-08 in HSCs

KAMMINGA_EZH2_TARGETS targets or partners of Ezh2 0.142857 5 35

GOCellularComponent 0.015374 0.047402 GO:0043596. The Y-shaped region of a nuclear replicating DNA mole

Genes annotated by the GO term

NUCLEAR_REPLICATION_FORK 0.1 1 10

GNF2_PCNA na

CancerGeneNeighborhood 4.93E-11 2.98E-09 0.177419 11 62

ChemicalGeneticPerturbations

MIDDLEAGE_DN 1.19E-06 1.11E-05 0.214286 3 14

Downregulated in fibroblasts from middle-age individuals, compared to young

GOBiologicalProcess

Genes 4.31E-04 GO term 0.1

DNA_DAMAGE_CHECKPOINT annotated by the 0.002113 GO:0000077. A signal2 20

transduction pathway, induced by DNA damag

na

GNF2_FEN1CancerGeneNeighborhood 1.76E-10 4.88E-09 0.12 6 50

ChemicalGeneticPerturbations

NEMETH_TNF_DN 1.31E-05 9.59E-05 0.1

Genes down-regulated after 3 h in LPS-stimulated RAW 3 30

2647 macrophages

ChemicalGeneticPerturbations

5.68E-08 7.01E-07

IRITANI_ADPROX_UP LEC-specific induced by AdProx-1 0.16 4 25

C na

GNF2_CKS1BancerGeneNeighborhood 2.61E-07 2.68E-06 0.111111 4 36

na

GNF2_CKS2CancerGeneNeighborhood 8.03E-09 1.19E-07 0.108696 5 46

GNF2_CDC20 na

CancerGeneNeighborhood 5.80E-11 2.57E-09 0.156863 8 51

ChemicalGeneticPerturbations any timepoint (4-24 hrs) following ectopic expression of p21 (CDKN1A) in OvCa cell

P21_P53_ANY_DN 5.73E-11 2.94E-09 0.181818

Down-regulated at 8 44

ChemicalGeneticPerturbations cancer cell lines reistant to doxorubicin, compared to parent chemosensitive lin

DOX_RESIST_GASTRIC_UP 4.04E-07

Upregulated in gastric 3.95E-06 0.1 4 40

na

GNF2_RFC3CancerGeneNeighborhood 3.43E-09 5.57E-08 0.128205 5 39

na

GNF2_RFC4CancerGeneNeighborhood 3.49E-10 8.02E-09 0.103448 6 58

ChemicalGeneticPerturbations

MTX_RES_XENOGRAFTS_UP 0.015374 0.047402 0.1 1 10

Up-regulation is correlated with resistance of human cancer xenografts to methotrexate

PARP_KO_DN Downregulated in MEF cells from PARP knockout mice 2

1.78E-04 9.13E-04 0.153846

ChemicalGeneticPerturbations 13

ChemicalGeneticPerturbations

LAMB_CYCLIN_D3_GLOCUS 2.40E-04 0.001209 0.133333 2 15

E2F target genes highly correlated with cyclin D3 expression (p = 0.002)

GNF2_H2AFX na

CancerGeneNeighborhood 1.06E-05 7.84E-05 0.107143 3 28

GNF2_BUB1B na

CancerGeneNeighborhood 3.48E-11 3.31E-09 0.173913 8 46

ChemicalGeneticPerturbations

1.04E-09 2.16E-08 0.16129 5

GOLDRATH_CELLCYCLECell cycle genes induced during antigen activation of CD8+ T cells. 31

C na

GNF2_RRM1ancerGeneNeighborhood 1.46E-11 2.43E-09 0.146341 12 82

C na

GNF2_RRM2ancerGeneNeighborhood 6.40E-11 2.37E-09 0.243243 9 37

ChemicalGeneticPerturbations hypermethylated promoters upregulated by the combination of TSA and DAC in ov

Genes with basally

TSADAC_HYPERMETH_HYPERAC_OVCA_UP 0.015374 0.047402 0.1 1 10

GNF2_CENPF na

CancerGeneNeighborhood 6.91E-11 2.19E-09 0.145455 8 55

CancerGeneNeighborhood

GNF2_CENPE na 6.40E-11 2.25E-09 0.189189 7 37

CanonicalPathwayPlk3 phosphorylates CDC25c,0.142857 the G2/M 1

PLK3PATHWAY Active 0.010786 0.03487 blocking 7

transition, and phosphorylates p53 to induce a

ChemicalGeneticPerturbationsH2O2, Menadione and t-BH in breast cancer cells

Downregulated by

OXSTRESS_BREASTCA_DN 2.77E-07 2.80E-06 0.333333 3 9

ChemicalGeneticPerturbations

Cell cycle- and proliferation-related 0.111111

UNDERHILL_PROLIFERATION 2 18

3.48E-04 0.00173 genes underexpressed in plasma cells.

ChemicalGeneticPerturbations

Genes involved with

0.015374 0.047402 0.1 1 10

FERRANDO_CHEMO_RESPONSE_PATHWAY chemotherapy response and drug targets which are upregulated in samples posit

ChemicalGeneticPerturbations

50 top ranked SAM-defined over-expressed genes in each subgroup

ZHAN_MM_CD138_PR_VS_REST 3.00E-09 5.26E-08 0.131579 5 38

CanonicalPathway

SRCRPTPPATHWAY Src by Protein-tyrosine 0.1

Activation of0.015374 0.047402 phosphatase alpha1 10

CanonicalPathwayactivates the cdc2/cyclin B complex to induce the G2/M transition.

SA_G2_AND_M_PHASES Cdc25 0.012317 0.038878 0.125 1 8

ChemicalGeneticPerturbations

1.41E-09 2.85E-08 0.151515 5 33

GREENBAUM_E2A_UP Table includes transcripts up-regulated 3-fold or greater in the E2A-deficient cell lines

ChemicalGeneticPerturbations late timepoints (20-24 hrs) following1ectopic expression of p21 (CDKN1A) in OvCa c

P21_P53_LATE_DN 0.013847 0.043295 0.111111

Down-regulated at 9

na

module_57CancerModules 2.95E-10 7.02E-09 0.107143 6 56

ChemicalGeneticPerturbations in multiple myeloma cells exposed to the pro-proliferative cytokine IL-6 versus tho

Genes upregulated

CROONQUIST_IL6_STARVE_UP 1.41E-09 2.85E-08 0.151515 5 33

CancerGeneNeighborhood

GNF2_SMC2L1 na 1.22E-07 1.46E-06 0.133333 4 30

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

na

GNF2_LYN CancerGeneNeighborhood 1.05E-08 8.64E-07 0.115385 3 26

CanonicalPathway expression by T cells induces apoptosis in Fas-expressing, inactive B cells.

BBCELLPATHWAY Fas ligand 2.20E-07 6.01E-06 0.5 2 4

CanonicalPathwayrequire interaction with helper T cells to produce2antigen-specific immunoglobulins as a key ele

ASBCELLPATHWAY B cells 1.03E-06 1.40E-05 0.25 8

IL5PATHWAY Pro-inflammatory IL-5 is secretes by activated T cells, eosinophils, 10 mast cells, and stimulates the p

CanonicalPathway 1.65E-06 1.50E-05 0.2 2 and

CanonicalPathway T subtype Th1 produces pro-inflammatory cytokines that stimulate phagocytosis, while Th2 cel

TH1TH2PATHWAY Helper 4.98E-06 3.14E-05 0.117647 2 17

CanonicalPathway

TCRAPATHWAY 2.02E-06 1.50E-05 0.181818 T 11

The kinases Lck and Fyn phosphorylate and activate the2 cell receptor, which recognizes antigen-boun

CanonicalPathway

CTLA4PATHWAY 5.60E-06 interaction with an antigen-MHC-I complex on an antigen-presenting cell (AP

T cell activation requires 3.28E-05 0.111111 2 18

CanonicalPathway

B 1.65E-06 histocompatibility complex (class II MHC), immunoglobulins, adhesion protei

BLYMPHOCYTEPATHWAYcells express the major1.50E-05 0.2 2 10

CanonicalPathway

EOSINOPHILSPATHWAY 1.03E-06 1.40E-05 0.25 2 in

Recruitment of eosinophils in the inflammatory response observed8 asthma occurs via the chemoatt

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

C na

module_219 ancerModules 6.67E-06 6.63E-05 0.12 3 25

ChemicalGeneticPerturbations

LIZUKA_L1_SM_G1 expressed 0.045542 0.111111 1 9

Genes highly0.013355 in well differentiated hepatocellular carcinoma vs. non-tumor liver with hepat

GNF2_CDC2 na

CancerGeneNeighborhood 2.35E-10 6.85E-09 0.109091 6 55

C na

module_315 ancerModules 2.23E-04 0.001475 0.133333 2 15

ChemicalGeneticPerturbations upregulated by E2F1 induction 2

E2F1_DNA_UP 1.17E-04

DNA replication genes 8.59E-04 0.181818 11

na

GNF2_FEN1CancerGeneNeighborhood 1.50E-10 5.10E-09 0.12 6 50

GOBiologicalProcess

Genes annotated by the GO term

9.58E-05 7.37E-04 0.2 2 10

MITOTIC_SPINDLE_ORGANIZATION_AND_BIOGENESIS GO:0007052. A process that is carried out at the cellular level which

ChemicalGeneticPerturbations

CMV_IE86_UP 1.02E-08 2.13E-07 0.1 5 50

Upregulated by expression of cytomegalovirus IE86 protein in primary human fibroblasts

GNF2_CDC20 na

CancerGeneNeighborhood 5.18E-11 3.02E-09 0.137255 7 51

ChemicalGeneticPerturbations

Genes 5.15E-06 multiple 0.130435 3 23

CROONQUIST_IL6_RAS_DN dowmregulated in5.52E-05 myeloma cells exposed to the pro-proliferative cytokine IL-6 versus

GNF2_CCNB2 na

CancerGeneNeighborhood 1.70E-10 5.54E-09 0.115385 6 52

ChemicalGeneticPerturbations cancer cell lines reistant to doxorubicin, compared to parent chemosensitive lin

DOX_RESIST_GASTRIC_UP 5.83E-11

Upregulated in gastric 2.80E-09 0.2 8 40

ChemicalGeneticPerturbations

Genes 8.47E-06 8.02E-05 0.111111

GENOTOXINS_ALL_4HRS_REGregulated in mouse lymphocytes (TK 3.7.2C) at 4 3 27

hours by all six genotoxins tested (cisplatin, m

CancerGeneNeighborhood

GNF2_SMC4L1 na 2.83E-11 3.29E-09 0.103896 8 77

C na

GNF2_ESPL1 ancerGeneNeighborhood 5.04E-11 3.43E-09 0.171429 6 35

GNF2_BUB1B na

CancerGeneNeighborhood 1.06E-10 4.13E-09 0.130435 6 46

GNF2_H2AFX na

CancerGeneNeighborhood 7.86E-08 1.49E-06 0.142857 4 28

ChemicalGeneticPerturbations

1.40E-04 timepoints (4-8 hrs) 2 12

P21_P53_EARLY_DN Down-regulated at early 9.94E-04 0.166667 following ectopic expression of p21 (CDKN1A) in OvCa ce

C na

module_320 ancerModules 3.61E-04 0.002196 0.105263 2 19

GNF2_MCM4 na

CancerGeneNeighborhood 5.77E-11 2.94E-09 0.16 8 50

C na

GNF2_RRM1ancerGeneNeighborhood 2.09E-11 3.41E-09 0.121951 10 82

GOCellularComponent 2.54E-04 0.001605 GO:0005876. Any microtubule that is part of a mitotic or meiotic spi

SPINDLE_MICROTUBULE Genes annotated by the GO term 0.125 2 16

C na

GNF2_RRM2ancerGeneNeighborhood 6.64E-11 3.01E-09 0.189189 7 37

GOBiologicalProcess

Genes annotated by the 8.59E-04 0.181818

1.17E-04 2 11

SPINDLE_ORGANIZATION_AND_BIOGENESIS GO term GO:0007051. A process that is carried out at the cellular level which

GNF2_MKI67 na

CancerGeneNeighborhood 7.53E-06 7.31E-05 0.115385 3 26

GNF2_CENPF na

CancerGeneNeighborhood 6.75E-11 2.89E-09 0.145455 8 55

GNF2_CENPE na

CancerGeneNeighborhood 2.18E-09 4.80E-08 0.135135 5 37

ChemicalGeneticPerturbationsDAC treatment in LD419 fibroblast cells

DAC_FIBRO_DN 8.42E-10 2.21E-08

Downregulated by 0.4 4 10

na

GNF2_TTK CancerGeneNeighborhood 5.04E-11 3.43E-09 0.171429 6 35

GNF2_CCNA2 na

CancerGeneNeighborhood 4.61E-11 3.76E-09 0.129032 8 62

GNF2_HMMR na

CancerGeneNeighborhood 7.06E-11 2.88E-09 0.159091 7 44

ChemicalGeneticPerturbations at 1.68E-09 0.11236

IDX_TSA_UP_CLUSTER3 4.13E-12 10 89

Strongly up-regulated 16-24 hours during differentiation of 3T3-L1 fibroblasts into adipocytes with I

ChemicalGeneticPerturbations

Putative 1.62E-09 3.87E-08 in HSCs

KAMMINGA_EZH2_TARGETS targets or partners of Ezh2 0.142857 5 35

ChemicalGeneticPerturbations

Genes involved with

9.58E-05 7.37E-04 0.2 2 10

FERRANDO_CHEMO_RESPONSE_PATHWAY chemotherapy response and drug targets which are upregulated in samples posit

ChemicalGeneticPerturbations

50 top ranked SAM-defined over-expressed genes in each subgroup

ZHAN_MM_CD138_PR_VS_REST 5.64E-11 3.07E-09 0.184211 7 38

GNF2_PCNA na

CancerGeneNeighborhood 4.61E-11 3.76E-09 0.129032 8 62

ChemicalGeneticPerturbations

1.18E-09 3.00E-08 0.151515 5 33

GREENBAUM_E2A_UP Table includes transcripts up-regulated 3-fold or greater in the E2A-deficient cell lines

ChemicalGeneticPerturbations late timepoints (20-24 hrs) following1ectopic expression of p21 (CDKN1A) in OvCa c

P21_P53_LATE_DN 0.013355 0.045542 0.111111

Down-regulated at 9

ChemicalGeneticPerturbations

4.01E-04 0.002402 ERM 2 20

ERM_KO_TESTES_DN Down-regulated in testes from 4 week old0.1 knockout mice, compared to wild-type controls

ChemicalGeneticPerturbations in multiple myeloma cells exposed to the pro-proliferative cytokine IL-6 versus tho

Genes upregulated

CROONQUIST_IL6_STARVE_UP 1.18E-09 3.00E-08 0.151515 5 33

ChemicalGeneticPerturbations

Down-regulated

2.23E-04 0.001475 0.133333 2 15

MMS_HUMAN_LYMPH_LOW_4HRS_DNat 4 hours following treatment of human lymphocytes (TK6) with a low dose of methy

ChemicalGeneticPerturbations in both ITTP and DP more than 3-fold, with average signal value differences of at

LEE_TCELLS3_UP 1.52E-11 3.09E-09 0.105263

Transcripts enriched 10 95

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

VLB_RES_XENOGRAFTS_UP 0.001989 0.015246 0.111111 1 9

Up-regulation is correlated with resistance of human cancer xenografts to vinblastine

ChemicalGeneticPerturbations

Oligodendroglia/myelination

4.40E-06 2.02E-04 0.125 2 16

ASTON_OLIGODENDROGLIA_MYELINATION_SUBSETrelated genes which are downregulated in major depressive disorder (p <

KEGG na

HSA00730_THIAMINE_METABOLISM 0.001768 0.016264 0.125 1 8

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GOBiologicalProcess

Genes annotated by the 0.044188

0.002209 GO 0.1 1 10

POSITIVE_REGULATION_OF_CYTOKINE_SECRETION term GO:0050715. Any process that activates or increases the frequency,

GOBiologicalProcess

Genes 0.002209 GO term 0.1 1 10

INTERLEUKIN_1_SECRETION annotated by the 0.044188 GO:0050701. The regulated release of interleukin-1 from a cell or gr

chr7q Positional na 0.001989 0.044744 0.111111 1 9

CanonicalPathway

PEPIPATHWAY (PEPI) induces epithelial cells to 1 7

Proepithelin 0.001547 0.039779 0.142857secrete IL-8, which promotes elastase secretion by neutro

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

na

module_21CancerModules 0.014828 0.046934 0.1 1 10

C na

module_315 ancerModules 1.33E-06 1.74E-05 0.2 3 15

GOBiologicalProcess

Genes annotated by the GO term

2.54E-04 0.125

MITOTIC_SISTER_CHROMATID_SEGREGATION 0.001449 GO:0000070. The cell 2 16

cycle process whereby replicated homologous

na

GNF2_FEN1CancerGeneNeighborhood 1.50E-10 1.15E-08 0.12 6 50

GOCellularComponent 3.23E-04 GO term 0.111111 2 18

REPLICATION_FORK Genes annotated by the 0.001771 GO:0005657. The Y-shaped region of a replicating DNA molecule, res

ChemicalGeneticPerturbations

CMV_IE86_UP 1.02E-08 2.81E-07 0.1 5 50

Upregulated by expression of cytomegalovirus IE86 protein in primary human fibroblasts

CanonicalPathway

PTC1PATHWAY 0.014828 0.046934 0.1 1 10

The binding of extracellular signaling protein Sonic hedgehog to the Patched receptor (Ptc1) allows pro

GNF2_CDC20 na

CancerGeneNeighborhood 1.56E-10 1.07E-08 0.117647 6 51

GOBiologicalProcess

Genes annotated by the 0.001614 0.117647

2.88E-04 GO 2 17

ESTABLISHMENT_OF_ORGANELLE_LOCALIZATION term GO:0051656. The directed movement of an organelle to a specific lo

GOBiologicalProcess

Genes annotated by the GO term 0.117647 2 17

SISTER_CHROMATID_SEGREGATION 2.88E-04 0.001614 GO:0000819. The process by which sister chromatids are organized a

GNF2_CCNB2 na

CancerGeneNeighborhood 1.70E-10 1.07E-08 0.115385 6 52

ChemicalGeneticPerturbations cancer cell lines reistant to doxorubicin, compared to parent chemosensitive lin

DOX_RESIST_GASTRIC_UP 5.85E-11

Upregulated in gastric 6.72E-09 0.175 7 40

ChemicalGeneticPerturbations

Coregulated and trans-regulated putative downstream targets of the cis-regulated HSC transcript, Fli1

BYSTRYKH_FLI1_TARGETS_GLOCUS 0.013355 0.043061 0.111111 1 9

Genes annotated by the 8.57E-08 0.131579 5 38

SPINDLE GOCellularComponent 2.48E-09 GO term GO:0005819. The array of microtubules and associated molecules th

GOBiologicalProcess

Genes annotated by the 0.001449 GO:0006270. The process by which DNA replication is started; this in

DNA_REPLICATION_INITIATION 2.54E-04 GO term 0.125 2 16

GNF2_H2AFX na

CancerGeneNeighborhood 9.47E-06 8.49E-05 0.107143 3 28

ChemicalGeneticPerturbations

1.20E-07 2.44E-06 0.129032 4

GOLDRATH_CELLCYCLECell cycle genes induced during antigen activation of CD8+ T cells. 31

GNF2_MCM4 na

CancerGeneNeighborhood 1.02E-08 2.81E-07 0.1 5 50

GOCellularComponent 1.20E-07 2.44E-06 0.129032

Genes annotated 4 of

CHROMOSOME__PERICENTRIC_REGION by the GO term GO:0000775. The central region31 a chromosome that includes the

C na

GNF2_RRM2ancerGeneNeighborhood 2.18E-09 7.91E-08 0.135135 5 37

GOCellularComponent 6.67E-06 GO term GO:0000776. A multisubunit complex that is located at the pericentr

KINETOCHORE Genes annotated by the 6.22E-05 0.12 3 25

GOBiologicalProcess

GENE_SILENCING 0.014828 GO term 0.1 1 10

Genes annotated by the 0.046934 GO:0016458. Any mechanism, at the level of transcription or post-tr

GNF2_CENPF na

CancerGeneNeighborhood 2.35E-10 1.25E-08 0.109091 6 55

C na

module_283 ancerModules 0.010402 0.034342 0.142857 1 7

chr4q27 Positional na 1.40E-04 8.42E-04 0.166667 2 12

GNF2_CENPE na

CancerGeneNeighborhood 2.51E-07 4.13E-06 0.108108 4 37

CanonicalPathway

CDC25PATHWAY 0.013355 0.043061 0.111111 1 9

The protein phosphatase Cdc25 is phosphorylated by Chk1 and activates Cdc2 to stimulate eukaryotic

na

GNF2_TTK CancerGeneNeighborhood 1.62E-09 6.97E-08 0.142857 5 35

ChemicalGeneticPerturbations

5.15E-06 5.07E-05 0.130435

P21_P53_MIDDLE_DN Down-regulated at intermediate timepoints (12-16 hrs) 3 ectopic expression of p21 (CDKN1A)

following 23

GNF2_HMMR na

CancerGeneNeighborhood 5.29E-09 1.74E-07 0.113636 5 44

ChemicalGeneticPerturbations

Genes involved with

9.58E-05 6.96E-04 0.2 2 10

FERRANDO_CHEMO_RESPONSE_PATHWAY chemotherapy response and drug targets which are upregulated in samples posit

GOCellularComponent 0.014828 0.046934 GO:0043596. The Y-shaped region of a nuclear replicating DNA mole

Genes annotated by the GO term

NUCLEAR_REPLICATION_FORK 0.1 1 10

CanonicalPathway

SRCRPTPPATHWAY Src by Protein-tyrosine 0.1

Activation of0.014828 0.046934 phosphatase alpha1 10

CanonicalPathwayactivates the cdc2/cyclin B complex to induce the G2/M transition.

SA_G2_AND_M_PHASES Cdc25 0.01188 0.038484 0.125 1 8

GOBiologicalProcess

Genes annotated by the 6.96E-04 0.2 2 10

CHROMOSOME_CONDENSATION 9.58E-05 GO term GO:0030261. The progressive compaction of dispersed interphase ch

ChemicalGeneticPerturbations

1.56E-07 2.91E-06 0.121212 4 33

GREENBAUM_E2A_UP Table includes transcripts up-regulated 3-fold or greater in the E2A-deficient cell lines

ChemicalGeneticPerturbations

4.01E-04 0.002161 ERM 2 20

ERM_KO_TESTES_DN Down-regulated in testes from 4 week old0.1 knockout mice, compared to wild-type controls

CancerGeneNeighborhood

GNF2_SMC2L1 na 1.05E-07 2.20E-06 0.133333 4 30

GOCellularComponent 1.99E-06 GO term GO:0000922. Either of the ends 17 a spindle, where spindle microtub

SPINDLE_POLE Genes annotated by the 2.33E-05 0.176471 3 of

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

9.43E-10 1.75E-08 0.135135 of 37

ADIP_DIFF_CLUSTER5 Strongly upregulated at 24 hours during differentiation 5 3T3-L1 fibroblasts into adipocytes (cluster 5

GNF2_CDC2 na

CancerGeneNeighborhood 8.05E-11 2.49E-09 0.163636 9 55

CanonicalPathway

PTC1PATHWAY 0.012644 0.047384 0.1 1 10

The binding of extracellular signaling protein Sonic hedgehog to the Patched receptor (Ptc1) allows pro

YU_CMYC_UP Myc-activated genes

8.98E-08 1.02E-06 0.117647

ChemicalGeneticPerturbations 4 34

ChemicalGeneticPerturbations

Genes 3.13E-06 multiple 0.130435 3 23

CROONQUIST_IL6_RAS_DN dowmregulated in2.86E-05 myeloma cells exposed to the pro-proliferative cytokine IL-6 versus

GNF2_CCNB2 na

CancerGeneNeighborhood 4.44E-11 2.75E-09 0.173077 9 52

ChemicalGeneticPerturbations

Genes 5.15E-06 4.55E-05 0.111111

GENOTOXINS_ALL_4HRS_REGregulated in mouse lymphocytes (TK 3.7.2C) at 4 3 27

hours by all six genotoxins tested (cisplatin, m

C na

GNF2_MSH2ancerGeneNeighborhood 4.58E-06 4.09E-05 0.115385 3 26

C na

GNF2_ESPL1 ancerGeneNeighborhood 6.98E-10 1.36E-08 0.142857 5 35

GOCellularComponent 1.39E-04 GO term GO:0005871. Any complex that 14

KINESIN_COMPLEX Genes annotated by the 8.92E-04 0.142857 2 includes a dimer of molecules from t

ChemicalGeneticPerturbations

3.92E-07 timepoints hrs) 3 12

P21_P53_EARLY_DN Down-regulated at early 4.10E-06 (4-8 0.25 following ectopic expression of p21 (CDKN1A) in OvCa ce

GNF2_MCM4 na

CancerGeneNeighborhood 1.05E-10 2.90E-09 0.12 6 50

GNF2_MKI67 na

CancerGeneNeighborhood 2.00E-10 4.93E-09 0.192308 5 26

CanonicalPathway

CDC25PATHWAY 0.011387 0.043777 0.111111 1 9

The protein phosphatase Cdc25 is phosphorylated by Chk1 and activates Cdc2 to stimulate eukaryotic

C na

module_283 ancerModules 0.008867 0.035184 0.142857 1 7

ChemicalGeneticPerturbationsDAC treatment in LD419 fibroblast cells

DAC_FIBRO_DN 0.012644 0.047384

Downregulated by 0.1 1 10

na

GNF2_TTK CancerGeneNeighborhood 1.01E-07 1.14E-06 0.114286 4 35

GNF2_CCNA2 na

CancerGeneNeighborhood 4.68E-11 2.31E-09 0.129032 8 62

GNF2_HMMR na

CancerGeneNeighborhood 7.03E-11 2.27E-09 0.136364 6 44

GNF2_PCNA na

CancerGeneNeighborhood 4.68E-11 2.48E-09 0.145161 9 62

ChemicalGeneticPerturbations

MIDDLEAGE_DN 6.47E-07 6.49E-06 0.214286 3 14

Downregulated in fibroblasts from middle-age individuals, compared to young

ChemicalGeneticPerturbations intermediate timepoints (12-16 hrs) 2

P21_MIDDLE_DN 1.39E-04 8.92E-04 0.142857

Down-regulated at 14

follwing ectopic expression of p21 (CDKN1A) in

ChemicalGeneticPerturbations upregulated by E2F1 induction 2

E2F1_DNA_UP 8.44E-05

DNA replication genes 5.50E-04 0.181818 11

C na

module_315 ancerModules 1.61E-04 0.001011 0.133333 2 15

na

GNF2_FEN1CancerGeneNeighborhood 4.33E-09 6.42E-08 0.1 5 50

ChemicalGeneticPerturbations

1.86E-10 4.76E-09

IRITANI_ADPROX_UP LEC-specific induced by AdProx-1 0.2 5 25

na

GNF2_CKS2CancerGeneNeighborhood 4.59E-11 2.62E-09 0.173913 8 46

C na

GNF2_CKS1BancerGeneNeighborhood 3.66E-11 3.87E-09 0.222222 8 36

GNF2_CDC20 na

CancerGeneNeighborhood 4.95E-11 2.04E-09 0.156863 8 51

ChemicalGeneticPerturbations any timepoint (4-24 hrs) following ectopic expression of p21 (CDKN1A) in OvCa cell

P21_P53_ANY_DN 2.25E-09 3.63E-08 0.113636

Down-regulated at 5 44

ChemicalGeneticPerturbations cancer cell lines reistant to doxorubicin, compared to parent chemosensitive lin

DOX_RESIST_GASTRIC_UP 1.76E-07

Upregulated in gastric 1.95E-06 0.1 4 40

na

GNF2_RFC3CancerGeneNeighborhood 4.89E-11 2.14E-09 0.179487 7 39

na

GNF2_RFC4CancerGeneNeighborhood 8.13E-11 2.32E-09 0.137931 8 58

GNF2_H2AFX na

CancerGeneNeighborhood 2.71E-10 6.49E-09 0.178571 5 28

ChemicalGeneticPerturbations

Sixty-nine genes commonly upregulated in undifferentiated cancer relative to well-differentiated canc

CANCER_UNDIFFERENTIATED_META_UP 3.92E-11 3.63E-09 0.121212 8 66

GOCellularComponent 0.011387 0.043777 GO:0030530. Particulate complex of heterogeneous nuclear RNA (hn

Genes annotated by the GO term 0.111111

HETEROGENEOUS_NUCLEAR_RIBONUCLEOPROTEIN_COMPLEX 1 9

GOCellularComponent 1.84E-04 0.001144 GO:0005876. Any microtubule that is part of a mitotic or meiotic spi

SPINDLE_MICROTUBULE Genes annotated by the GO term 0.125 2 16

C na

GNF2_RRM1ancerGeneNeighborhood 2.76E-11 6.83E-09 0.109756 9 82

C na

GNF2_RRM2ancerGeneNeighborhood 6.27E-11 2.33E-09 0.162162 6 37

GNF2_CENPF na

CancerGeneNeighborhood 8.05E-11 2.49E-09 0.163636 9 55

GNF2_CENPE na

CancerGeneNeighborhood 6.27E-11 2.33E-09 0.162162 6 37

ChemicalGeneticPerturbationsH2O2, Menadione and t-BH in breast cancer cells

OXSTRESS_BREASTCA_DN 5.54E-05 3.73E-04 0.222222

Downregulated by 2 9

ChemicalGeneticPerturbations

Genes involved with

0.012644 0.047384 0.1 1 10

FERRANDO_CHEMO_RESPONSE_PATHWAY chemotherapy response and drug targets which are upregulated in samples posit

ChemicalGeneticPerturbations

50 top ranked SAM-defined over-expressed genes in each subgroup

ZHAN_MM_CD138_PR_VS_REST 4.21E-11 2.84E-09 0.157895 6 38

CanonicalPathway

SRCRPTPPATHWAY Src by Protein-tyrosine 0.1

Activation of0.012644 0.047384 phosphatase alpha1 10

CanonicalPathwayactivates the cdc2/cyclin B complex to induce the G2/M transition.

SA_G2_AND_M_PHASES Cdc25 0.010128 0.039344 0.125 1 8

C na

module_467 ancerModules 0.008867 0.035184 0.142857 1 7

ChemicalGeneticPerturbations

7.93E-08 9.49E-07 0.121212 4 33

GREENBAUM_E2A_UP Table includes transcripts up-regulated 3-fold or greater in the E2A-deficient cell lines

ChemicalGeneticPerturbations late timepoints (20-24 hrs) following1ectopic expression of p21 (CDKN1A) in OvCa c

P21_P53_LATE_DN 0.011387 0.043777 0.111111

Down-regulated at 9

ChemicalGeneticPerturbations in multiple myeloma cells exposed to the pro-proliferative cytokine IL-6 versus tho

Genes upregulated

CROONQUIST_IL6_STARVE_UP 5.04E-10 1.04E-08 0.151515 5 33

CancerGeneNeighborhood

GNF2_SMC2L1 na 3.57E-10 8.04E-09 0.166667 5 30

ChemicalGeneticPerturbations in both ITTP and DP more than 3-fold, with average signal value differences of at

LEE_TCELLS3_UP 2.40E-11 8.91E-09 0.136842

Transcripts enriched 13 95

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

Top 8.41E-05 0.001978 0.166667 2 12

SARCOMAS_SYNOVIAL_DN 20 negative significant genes associated with synovial sarcomas, versus other soft-tissue tumors.

microRNATargets

CGGTGTG,MIR-220 na 0.006946 0.047279 0.166667 1 6

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GOBiologicalProcess

Genes annotated

1.26E-04 GO term 0.117647 2 17

REGULATION_OF_ACTION_POTENTIAL by the 0.009597 GO:0001508. Any process that modulates the frequency, rate or ext

ChemicalGeneticPerturbations

Oligodendroglia/myelination

1.11E-04 0.009885 0.125 2 16

ASTON_OLIGODENDROGLIA_MYELINATION_SUBSETrelated genes which are downregulated in major depressive disorder (p <

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GOMolecularFunction 3.89E-05 0.001707 GO:0005509. Interacting selectively with calcium ions (Ca2+).

CALCIUM_ION_BINDING Genes annotated by the GO term 0.137255 14 102

ChemicalGeneticPerturbations nucleus accumbens of mice after 2 weeks of induction of transgenic deltaFosB

DFOSB_BRAIN_2WKS_UP in the

Up-regulated 6.96E-06 4.55E-04 0.25 9 36

CanonicalPathway

GABAPATHWAY 8.67E-04 0.017661 0.333333 4 12

Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter whose receptor is regulated by Pli

CanonicalPathway

NOS1PATHWAY 4.88E-04 0.011868 0.277778 5 18

Glutamate stimulates NMDA-mediates calcium influx, which promotes nitric oxide synthesis from argi

GOBiologicalProcess

Genes annotated by the 2.35E-08 0.125 46 368

NEUROLOGICAL_SYSTEM_PROCESS 8.84E-11 GO term GO:0050877. The processes pertaining to the functions of the nervo

GOBiologicalProcess

Genes annotated by the 0.013976 GO:0003001.

6.06E-04 GO term 0.214286 6 28

GENERATION_OF_A_SIGNAL_INVOLVED_IN_CELL_CELL_SIGNALING The cellular process by which a physical entity or chan

GOBiologicalProcess

METAL_ION_TRANSPORT 0.001698 GO term 0.104348 12 115

Genes annotated by the 0.028359 GO:0030001. The directed movement of metal ions, any metal ion w

CanonicalPathway

DAG (diacylglycerol) signaling activity

SA_DIACYLGLYCEROL_SIGNALING 3.91E-04 0.010082 0.4 4 10

ChemicalGeneticPerturbations

5.67E-04 0.013564 in the neocortex of 7

NOVA2_KO_SPLICING Genes that are alternatively spliced 0.184211 38

mice deficient in the neuron-specific splicing fa

GOMolecularFunction 3.30E-05 GO term 0.454545

Genes 5 11

GABA_RECEPTOR_ACTIVITY annotated by the 0.001513 GO:0016917. Combining with gamma-aminobutyric acid (GABA, 4-am

ChemicalGeneticPerturbations

Genes upregulated

0.002624 the crb 0.129032 8

SHEPARD_GENES_COMMON_BW_CB_MOin both 0.0388 mutant and bymb morpholino in zebra fish 62

GOBiologicalProcess

Genes annotated by the 0.009582 GO:0006813. The directed movement of potassium ions (K+) into, ou

POTASSIUM_ION_TRANSPORT 3.67E-04 GO term 0.155172 9 58

YU_CMYC_UP Myc-activated genes

4.15E-06 2.91E-04 0.264706

ChemicalGeneticPerturbations 9 34

GNF2_CCNB2 na

CancerGeneNeighborhood 5.26E-07 5.00E-05 0.230769 12 52

GOMolecularFunction 2.31E-04 GO term 0.116667

Genes 14 120

GATED_CHANNEL_ACTIVITY annotated by the 0.006872 GO:0022836. Catalysis of the transmembrane transfer of a solute by

GOMolecularFunction 5.47E-05 0.002185 0.416667

Genes annotated by the GO term

INWARD_RECTIFIER_POTASSIUM_CHANNEL_ACTIVITY GO:0005242. 5 12

Genes annotated by the GO term 0.184211 7 38

SPINDLE GOCellularComponent 5.67E-04 0.013564 GO:0005819. The array of microtubules and associated molecules th

CancerGeneNeighborhood

GNF2_TM4SF2 na 2.14E-11 8.56E-09 0.636364 14 22

C na

GNF2_ESPL1 ancerGeneNeighborhood 5.53E-07 5.13E-05 0.285714 10 35

microRNATargets

CAATGCA,MIR-33 na 6.46E-04 0.014257 0.123596 11 89

C na

module_438 ancerModules 0.00354 0.048228 0.123077 8 65

GNF2_MCM4 na

CancerGeneNeighborhood 3.32E-07 3.31E-05 0.24 12 50

C na

MORF_THRAancerGeneNeighborhood 9.67E-05 0.003386 0.183673 9 49

GOBiologicalProcess

NEURITE_DEVELOPMENT 1.34E-04 GO term 0.176471 9 51

Genes annotated by the 0.004372 GO:0031175. The process whose specific outcome is the progression

GNF2_RTN1 na

CancerGeneNeighborhood 6.00E-11 2.00E-08 0.333333 15 45

GOBiologicalProcess

NEURON_DEVELOPMENT 4.19E-04 GO term 0.152542 9 59

Genes annotated by the 0.010446 GO:0048666. The process whose specific outcome is the progression

ChemicalGeneticPerturbations

These are 3.04E-04 0.008491 0.104575 as 153

LI_FETAL_VS_WT_KIDNEY_DN genes identified by simple statistical criteria16 differing in their mRNA expresssion between

GenMAPP na

GLUTAMATE_METABOLISM 0.001994 0.031846 0.208333 5 24

GNF2_MKI67 na

CancerGeneNeighborhood 2.20E-08 2.83E-06 0.384615 10 26

CanonicalPathway hypertrophy is induced by NF-ATc4 and GATA4, 7

NFATPATHWAY Cardiac 0.002672 0.039216 0.142857 which are49stimulated through calcineurin activ

CanonicalPathway functions as a second messenger activating the7

CACAMPATHWAY Calcium 8.59E-08 9.53E-06 0.583333 12

calcium/calmodulin-dependent kinases, which

ChemicalGeneticPerturbations 0 0 0.230769

AGEING_BRAIN_DN Age-downregulated in the human frontal cortex 27 117

na

GNF2_TTK CancerGeneNeighborhood 3.34E-04 0.009145 0.2 7 35

CanonicalPathway

Some Wnt glycoprotein/Frizzled receptor interactions increase intracellular calcium and decrease cGM

ST_WNT_CA2_CYCLIC_GMP_PATHWAY 6.41E-04 0.01421 0.263158 5 19

GNF2_CCNA2 na

CancerGeneNeighborhood 1.10E-09 1.91E-07 0.258065 16 62

GOBiologicalProcess

AXON_GUIDANCE 0.001051 GO term 0.238095 5 21

Genes annotated by the 0.019891 GO:0007411. The process by which the migration of an axon growth

GenMAPP na

G_PROTEIN_SIGNALING 2.80E-07 2.87E-05 0.179775 16 89

microRNATargets

AGGTGCA,MIR-500 na 0.003761 0.049711 0.1125 9 80

GCM_MAPK10 na

CancerGeneNeighborhood 4.40E-05 0.001868 0.153846 12 78

GOMolecularFunction 3.91E-04 0.010082 GO:0008067.

Genes annotated by the GO term 0.4 4 10

METABOTROPIC_GLUTAMATE__GABA_B_LIKE_RECEPTOR_ACTIVITY A G-protein coupled receptor that is structurally/funct

GNF2_PCNA na

CancerGeneNeighborhood 3.86E-06 2.75E-04 0.193548 12 62

GNF2_DNM1 na

CancerGeneNeighborhood 0 0 0.42029 29 69

CanonicalPathway

NDKDYNAMINPATHWAY 2.65E-04 Phosphins 0.3125

Endocytotic role of NDK,0.007507 and Dynamin 5 16

ChemicalGeneticPerturbations classic

Genes expressed in

0.003653 0.048778 0.153846

POMEROY_DESMOPLASIC_VS_CLASSIC_MD_DN medulloblastomas. (p < 0.01) 6 39

GOBiologicalProcess

Genes annotated by the 3.41E-07 0.10992 41 373

NERVOUS_SYSTEM_DEVELOPMENT 2.05E-09 GO term GO:0007399. The process whose specific outcome is the progression

Genes annotated by the GO term 0.259259 7 27

SYNAPSE GOCellularComponent 5.79E-05 0.002221 GO:0045202. The junction between a nerve fiber of one neuron and

GOBiologicalProcess

Genes annotated by the 0.048497 GO:0007215. The series of molecular signals generated as a consequ

GLUTAMATE_SIGNALING_PATHWAY 0.003572 GO term 0.235294 4 17

TransfacTargets

YGTCCTTGR_UNKNOWN na 6.17E-04 0.013907 0.133333 10 75

C na

module_214 ancerModules 4.92E-04 0.0119 0.222222 6 27

C na

module_215 ancerModules 1.24E-05 6.96E-04 0.4 6 15

ChemicalGeneticPerturbations

TGFBETA_ALL_UP 5.01E-05 treatment of skin fibroblasts, at any timepoint

Upregulated by TGF-beta 0.00206 0.151899 12 79

KEGG na

HSA04512_ECM_RECEPTOR_INTERACTION2.75E-08 3.43E-06 0.197674 17 86

C na

GNF2_CKS1BancerGeneNeighborhood 0.002406 0.036806 0.166667 6 36

CancerGeneNeighborhood

GNF2_CDC20 na 4.19E-07 4.08E-05 0.235294 12 51

GOBiologicalProcess

Genes 9.33E-04 GO term 0.126582 10 79

GENERATION_OF_NEURONS annotated by the 0.018256 GO:0048699. The process by which nerve cells are generated. This in

GOMolecularFunction 1.10E-04 GO term 0.150685

Genes annotated 11 73

VOLTAGE_GATED_CHANNEL_ACTIVITY by the 0.003701 GO:0022832. Catalysis of the transmembrane transfer of a solute by

C na

module_563 ancerModules 1.24E-05 6.96E-04 0.4 6 15

ChemicalGeneticPerturbations

BRCA_PROGNOSIS_NEG expression is consistently 0.125

Genes whose5.87E-04 0.013616 11

negatively correlated with88breast cancer outcomes - higher ex

TransfacTargets

V$SMAD4_Q6 na 2.36E-05 0.001209 0.111111 20 180

CancerGeneNeighborhood

GNF2_SMC4L1 na 1.80E-04 0.005528 0.142857 11 77

ChemicalGeneticPerturbations

Poor prognosis marker genes in

0.002906 0.04188 0.126984 8 63

VANTVEER_BREAST_OUTCOME_GOOD_VS_POOR_DN Breast Cancer (part of NKI-70) from Van't Veer et al 2002

CanonicalPathway enhancer factor MEF2 activates0.25

HDACPATHWAY Myocyte 7.46E-05 0.002707 7 28

transcription of genes required for muscle cell differentiation

V$MSX1_01 na

TransfacTargets 5.26E-05 0.002119 0.116438 17 146

ChemicalGeneticPerturbations

E2F target genes highly correlated with cyclin D3 expression (p = 0.002)

LAMB_CYCLIN_D3_GLOCUS 0.002179 0.034517 0.266667 4 15

microRNATargets

GTACAGG,MIR-486 na 0.002672 0.039216 0.142857 7 49

C na

GNF2_RRM1ancerGeneNeighborhood 1.53E-05 8.03E-04 0.158537 13 82

C na

GNF2_RRM2ancerGeneNeighborhood 8.88E-06 5.45E-04 0.243243 9 37

na

V$NRSF_01TransfacTargets 0 0 0.263158 20 76

ChemicalGeneticPerturbations genes CLUSTER 1 The listed

target 9 63

VERNELL_PRB_CLSTR1 pRB pathway 6.87E-04 0.014828 0.142857 genes were found regulated by pRB and p16 and one

ChemicalGeneticPerturbations in multiple myeloma cells exposed to the pro-proliferative cytokine IL-6 versus tho

Genes upregulated

CROONQUIST_IL6_STROMA_UP 5.69E-05 0.002207 0.222222 8 36

na

V$OCT1_02TransfacTargets 1.74E-04 0.005414 0.102273 18 176

na

module_11CancerModules 2.26E-10 4.30E-08 0.154286 81 525

CancerGeneNeighborhood

GNF2_CENPF na 6.99E-06 4.50E-04 0.2 11 55

GNF2_AF1Q na

CancerGeneNeighborhood 8.27E-04 0.017289 0.25 5 20

CancerGeneNeighborhood

GNF2_CENPE na 4.79E-04 0.011725 0.189189 7 37

GOMolecularFunction 6.86E-04 0.01488 0.131579

Genes annotated by 10 76

PROTEIN_HETERODIMERIZATION_ACTIVITY the GO term GO:0046982. Interacting selectively with a nonidentical protein to fo

na

V$ATF1_Q6TransfacTargets 1.26E-05 6.91E-04 0.112299 21 187

C na

module_100 ancerModules 2.14E-10 4.28E-08 0.147727 78 528

microRNATargets

CACCAGC,MIR-138 na 6.52E-05 0.002431 0.106742 19 178

ChemicalGeneticPerturbations

50 top ranked SAM-defined over-expressed genes in each subgroup

ZHAN_MM_CD138_PR_VS_REST 1.28E-06 1.02E-04 0.263158 10 38

TransfacTargets

CTGRYYYNATT_UNKNOWN na 0.003765 0.049609 0.134615 7 52

na

V$EGR2_01TransfacTargets 1.80E-06 1.38E-04 0.131579 20 152

TransfacTargets

V$HAND1E47_01 na 4.36E-05 0.001872 0.103448 21 203

ChemicalGeneticPerturbations

transcripts up-regulated 3-fold 6 33

GREENBAUM_E2A_UP Table includes0.00151 0.02644 0.181818 or greater in the E2A-deficient cell lines

GOBiologicalProcess

Genes annotated by the 0.028237 GO:0045055. The regulated secretory pathway is a second secretory

REGULATED_SECRETORY_PATHWAY 0.001648 GO term 0.285714 4 14

TransfacTargets

na

CAGNWMCNNNGAC_UNKNOWN 9.62E-09 1.32E-06 0.225352 16 71

GenMAPP na 1.24E-11

CALCIUM_REGULATION_IN_CARDIAC_CELLS 5.50E-09 0.185185 25 135

na

V$ZF5_01 TransfacTargets 1.10E-04 0.003705 0.102703 19 185

CancerGeneNeighborhood

GNF2_SMC2L1 na 1.20E-04 0.003987 0.233333 7 30

GOBiologicalProcess

AXONOGENESIS 1.52E-04 GO term 0.195122 8 41

Genes annotated by the 0.004878 GO:0007409. Generation of a long process of a neuron, that carries

CanonicalPathway receptor is a G-protein coupled receptor in neutrophils that recognizes formylated bacterial

FMLPPATHWAY The fMLP 0.001774 0.029391 0.176471 6 34

KEGG na 1.05E-10

HSA04020_CALCIUM_SIGNALING_PATHWAY 2.63E-08 0.167665 28 167

GOBiologicalProcess

EXOCYTOSIS 2.47E-04 GO term 0.25 6 24

Genes annotated by the 0.007145 GO:0006887. The release of intracellular molecules (e.g. hormones,

TransfacTargets

GTGGGTGK_UNKNOWN na 2.01E-05 0.001043 0.103139 23 223

ChemicalGeneticPerturbations

BRG1_SW13_UP by transient expression of BRG1 at 24 hours in human, BRG1-lacking SW-13 cells

Up-regulated0.003005 0.042539 0.14 7 50

GNF2_CDC2 na

CancerGeneNeighborhood 1.53E-08 2.04E-06 0.254545 14 55

KEGG na

HSA04720_LONG_TERM_POTENTIATION 3.68E-05 0.00163 0.169231 11 65

GOMolecularFunction 4.01E-04 0.010208 GO:0005249. Catalysis of the transmembrane transfer of a potassium

Genes annotated by the GO term 0.194444

VOLTAGE_GATED_POTASSIUM_CHANNEL_ACTIVITY 7 36

GOMolecularFunction 3.14E-04 GO term

Genes annotated by 0.24 6 25

AUXILIARY_TRANSPORT_PROTEIN_ACTIVITYthe 0.008716 GO:0015457. Facilitates transport across one or more biological mem

GOBiologicalProcess

Genes annotated by the 0.018274 0.11828

9.38E-04 GO 11 93

MONOVALENT_INORGANIC_CATION_TRANSPORT term GO:0015672. The directed movement of inorganic cations with a val

GOBiologicalProcess

Genes 4.43E-04 GO term 0.138889 10 72

NEURON_DIFFERENTIATION annotated by the 0.010976 GO:0030182. The process whereby a relatively unspecialized cell acq

GOMolecularFunction 4.26E-05 GO term 0.166667

Genes annotated by the 11 66

VOLTAGE_GATED_CATION_CHANNEL_ACTIVITY0.001848 GO:0022843. Catalysis of the transmembrane transfer of a cation by

ChemicalGeneticPerturbations

1.07E-06 treatment 0.23913 at 46

TGFBETA_EARLY_UP Upregulated by TGF-beta8.91E-05 of skin fibroblasts11 30 min (clusters 1-3)

ChemicalGeneticPerturbations

Top 8.67E-04 0.017661 0.333333 4 12

SARCOMAS_SYNOVIAL_UP 20 positive significant genes associated with synovial sarcomas, versus other soft-tissue tumors.

TransfacTargets

V$AHRARNT_01 na 0.002526 0.037762 0.104762 11 105

TransfacTargets

YTAAYNGCT_UNKNOWN na 0.001829 0.030164 0.103448 12 116

ChemicalGeneticPerturbations in the absence of E2F1 and E2F2 14

IGLESIAS_E2FMINUS_UP 7.16E-04 0.015293 0.104478

Genes that increase 134

ChemicalGeneticPerturbations nucleus accumbens of mice after 2 weeks of induction of transgenic CREB

CREB_BRAIN_2WKS_UP in the

Up-regulated 2.50E-05 0.00123 0.291667 7 24

GNF2_BUB1 na

CancerGeneNeighborhood 3.35E-05 0.00152 0.28 7 25

TransfacTargets

V$MEIS1BHOXA9_01 na 0.003151 0.043833 0.101852 11 108

CMV_ALL_DN Downregulated at any 0.00156 0.138614

3.48E-05

ChemicalGeneticPerturbations timepoint following infection of14 101

primary human foreskin fibroblasts with CMV

C na

module_289 ancerModules 0.002437 0.036991 0.1 12 120

microRNATargets

TCTCTCC,MIR-185 na 3.35E-04 0.009101 0.125 12 96

TransfacTargets

V$MYB_Q5_01 na 3.01E-05 0.001398 0.106061 21 198

CanonicalPathway a benzodiazepine receptor antagonist that5may induce protective preconditioning in isch

FLUMAZENILPATHWAYFlumazenil is 9.60E-06 5.63E-04 0.555556 9

GOBiologicalProcess 2.79E-11 1.01E-08 0.123116 49

CELL_CELL_SIGNALING Genes annotated by the GO term GO:0007267. Any process that398 mediates the transfer of information

ChemicalGeneticPerturbations

CMV_24HRS_DN 2.49E-06 1.81E-04 0.185714

Downregulated at 24hrs following infection of primary13 70

human foreskin fibroblasts with CMV

na

module_2 CancerModules 7.64E-10 1.39E-07 0.112 42 375

T na

V$CART1_01ransfacTargets 1.40E-04 0.004532 0.104046 18 173

C na

module_381 ancerModules 2.12E-09 3.39E-07 0.666667 8 12

ChemicalGeneticPerturbations

Down-regulated 0.00151 0.02644 0.181818 6 33

CMV_HCMV_TIMECOURSE_4HRS_DN in fibroblasts following infection with human cytomegalovirus (at least 3-fold, with Af

C na

module_497 ancerModules 9.44E-07 8.19E-05 0.310345 9 29

GOBiologicalProcess

NEUROGENESIS 0.00233 GO term 0.11236 10 89

Genes annotated by the 0.036057 GO:0022008. Generation of cells within the nervous system.

GNF2_HMMR na

CancerGeneNeighborhood 7.15E-08 8.15E-06 0.272727 12 44

TransfacTargets

ACCTGTTG_UNKNOWNna 7.21E-04 0.015303 0.109244 13 119

ChemicalGeneticPerturbations

BASSO_HCL_DIFF 0.001371 0.02444 The analysis 10 83

Identification of HCL-specific genes, 0.120482 identified 89 genes that are differentially expressed in

ChemicalGeneticPerturbations

IRITANI_ADPROX_LYMPH 9

LYMPHATIC EC.69E-07 8.23E-05 0.14876 18 121

C na

GNF2_MAPTancerGeneNeighborhood 6.97E-11 2.14E-08 0.368421 14 38

GOMolecularFunction 6.13E-04 GO term 0.111111

Genes 13 117

CATION_CHANNEL_ACTIVITY annotated by the 0.013904 GO:0005261. Catalysis of the energy-independent passage of cation

ChemicalGeneticPerturbations

TGFBETA_C1_UP 1.08E-06 treatment skin fibroblasts, cluster 1 16

Upregulated by TGF-beta8.82E-05 of0.4375 7

ChemicalGeneticPerturbations in Egr2Lo/Lo mice (who bear mutations in the 90

LE_MYELIN_UP 8.79E-09 1.25E-06

Genes upregulated 0.2 18 transcription factor Egr2 and in whic

ChemicalGeneticPerturbations 0

ALZHEIMERS_DISEASE_DN 0 0.110793 Disease, in the CA1 region of the hippocampus

Downregulated in correlation with overt Alzheimer's 116 1047

TransfacTargets

YRTCANNRCGC_UNKNOWN na 0.002672 0.039216 0.142857 7 49

GOMolecularFunction 7.16E-05 0.002621 GO:0043169. Interacting selectively with cations, charged atoms or g

CATION_BINDING Genes annotated by the GO term 0.1 21 210

KEGG na 2.04E-06 1.54E-04 0.109244

HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION 26 238

CanonicalPathway a G-protein coupled receptor expressed in macrophages that recognizes chemokine ligands an

CCR5PATHWAY CCR5 is 0.002179 0.034517 0.266667 4 15

GOMolecularFunction 1.30E-04 GO term 0.357143

Genes annotated by the

POTASSIUM_CHANNEL_REGULATOR_ACTIVITY 0.004277 GO:0015459. 5 14

ChemicalGeneticPerturbations

Cell-cycle 2.99E-05 0.001403 0.126984 16 126

SERUM_FIBROBLAST_CELLCYCLE dependent genes regulated following exposure to serum in a variety of human fibroblast cel

C na

module_274 ancerModules 0 0 0.308642 25 81

C na

module_316 ancerModules 2.11E-06 1.56E-04 0.188406 13 69

GOMolecularFunction

Genes annotated by the GO term 0.25 5 20

GLUTAMATE_RECEPTOR_ACTIVITY 8.27E-04 0.017289 GO:0008066. Combining with glutamate to initiate a change in cell a

na

GNF2_FEN1CancerGeneNeighborhood 6.26E-04 0.013965 0.16 8 50

CanonicalPathway is expressed in skeletal muscle, heart muscle, and brown fat, and is a coactivator for receptors

PGC1APATHWAY PCG-1a 3.67E-08 4.31E-06 0.428571 9 21

na

GNF2_CKS2CancerGeneNeighborhood 0.00184 0.030234 0.152174 7 46

GOMolecularFunction 4.41E-05 0.001851 GO:0046873.

Genes annotated by the GO term 17 144

METAL_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 0.118056 Catalysis of the transfer of metal ions from one side of

GOBiologicalProcess

Genes annotated

1.13E-10 2.65E-08 0.221622 41 185

TRANSMISSION_OF_NERVE_IMPULSE by the GO term GO:0019226. The sequential electrochemical polarization and depol

C na

module_137 ancerModules 2.04E-10 4.29E-08 0.149338 79 529

ChemicalGeneticPerturbations any timepoint (4-24 hrs) following ectopic expression of p21 (CDKN1A) in OvCa cell

P21_P53_ANY_DN 0.001409 0.024996 0.159091

Down-regulated at 7 44

GOCellularComponent 8.61E-05 0.003041 GO:0044456. The junction between a nerve fiber of one neuron and

SYNAPSE_PART Genes annotated by the GO term 0.384615 5 13

GOBiologicalProcess

Genes 7.40E-11 2.11E-08 0.235294 40 170

SYNAPTIC_TRANSMISSION annotated by the GO term GO:0007268. The process of communication from a neuron to a targ

ChemicalGeneticPerturbations cancer cell lines reistant to doxorubicin, compared to parent chemosensitive lin

DOX_RESIST_GASTRIC_UP 7.84E-04

Upregulated in gastric 0.016555 0.175 7 40

microRNATargets

na

CACTGCC,MIR-34A,MIR-34C,MIR-449 8.36E-06 5.22E-04 0.101167 26 257

C na

module_141 ancerModules 0.002817 0.040742 0.25 4 16

GNF2_CDH11 na

CancerGeneNeighborhood 0.002414 0.036787 0.2 5 25

GNF2_BUB1B na

CancerGeneNeighborhood 1.23E-07 1.32E-05 0.26087 12 46

GNF2_H2AFX na

CancerGeneNeighborhood 6.06E-04 0.013976 0.214286 6 28

ChemicalGeneticPerturbations

Sixty-nine genes commonly upregulated in undifferentiated cancer relative to well-differentiated canc

CANCER_UNDIFFERENTIATED_META_UP 9.69E-04 0.018785 0.136364 9 66

na

module_66CancerModules 1.76E-10 3.90E-08 0.145794 78 535

GOMolecularFunction

Genes annotated by the GO term 0.14 7 50

POTASSIUM_CHANNEL_ACTIVITY 0.003005 0.042539 GO:0005267. Catalysis of facilitated diffusion of a potassium ion (by

microRNATargets

ACTGCCT,MIR-34B na 2.79E-05 0.001327 0.106599 21 197

C na

module_524 ancerModules 8.94E-04 0.017748 0.2 6 30

ChemicalGeneticPerturbations at 1.21E-04 0.168539

IDX_TSA_UP_CLUSTER3 1.55E-06 15 89

Strongly up-regulated 16-24 hours during differentiation of 3T3-L1 fibroblasts into adipocytes with I

GNF2_RAB3A na

CancerGeneNeighborhood 3.52E-08 4.25E-06 0.323529 11 34

GOBiologicalProcess

Genes annotated by the GO term GO:0000904.

6.87E-05 0.00254 9 47

CELLULAR_MORPHOGENESIS_DURING_DIFFERENTIATION 0.191489 The change in form (cell shape and size) that occurs wh

ChemicalGeneticPerturbations nucleus accumbens of mice after 8 weeks of induction of transgenic CREB

CREB_BRAIN_8WKS_UP in the

Up-regulated 8.13E-07 7.21E-05 0.189189 14 74

ChemicalGeneticPerturbations

Genes upregulated

3.51E-04 0.009406 0.142857 10

CORDERO_KRAS_KD_VS_CONTROL_UP in kras knockdown vs control in a human cell line 70

GOCellularComponent 0.001648 0.028237 GO:0008021. Secretory organelles, some 50 nm in diameter, of pres

SYNAPTIC_VESICLE Genes annotated by the GO term 0.285714 4 14

na

module_54CancerModules 1.42E-05 7.54E-04 0.100402 25 249

GOMolecularFunction

Genes annotated by the GO term

CHANNEL_REGULATOR_ACTIVITY 1.91E-04 0.005747 GO:0016247. 0.26087 6 23

GOBiologicalProcess

Genes annotated by the GO term 0.333333 4 12

NEUROTRANSMITTER_SECRETION 8.67E-04 0.017661 GO:0007269. The regulated release of neurotransmitter into the syn

ChemicalGeneticPerturbations in both ITTP and DP more than 3-fold, with average signal value differences of at

LEE_TCELLS3_UP 7.05E-07 6.40E-05 0.168421

Transcripts enriched 16 95

GenMAPP na

SMOOTH_MUSCLE_CONTRACTION 1.41E-05 7.60E-04 0.128788 17 132

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

Oligodendroglia/myelination

3.16E-07 1.18E-04 0.1875 3 16

ASTON_OLIGODENDROGLIA_MYELINATION_SUBSETrelated genes which are downregulated in major depressive disorder (p <

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway produced by Th20.029215 0.142857 the T cell 1

IL-13 is

ST_INTERLEUKIN_13_PATHWAY 0.005405 cells on activation of 7

antigen receptor, and by mast and basophil ce

ChemicalGeneticPerturbations

Top 3.65E-05 4.88E-04 0.166667 2 12

SARCOMAS_SYNOVIAL_DN 20 negative significant genes associated with synovial sarcomas, versus other soft-tissue tumors.

CanonicalPathway

B 0.006945 interact 0.111111 1 9

LYMPHOCYTEPATHWAY and T cell lymphocytes0.035033with other cells via transmembrane adhesion proteins such as CD44,

GOBiologicalProcess

LEUKOCYTE_MIGRATION 6.63E-05 8.36E-04 0.125 2

Genes annotated by the GO term GO:0050900. The movement of 16 leukocytes within or between differ

CanonicalPathway T subtype Th1 produces pro-inflammatory cytokines that stimulate phagocytosis, while Th2 cel

TH1TH2PATHWAY Helper 7.51E-05 9.22E-04 0.117647 2 17

GOBiologicalProcess

Genes 4.32E-05 5.60E-04 0.153846 2 a

LEUKOCYTE_CHEMOTAXIS annotated by the GO term GO:0030595. The movement of 13leukocyte in response to an extern

C na

module_478 ancerModules 9.44E-05 0.001071 0.105263 2 19

na

GNF2_FGR CancerGeneNeighborhood 7.97E-09 3.62E-07 0.125 4 32

CanonicalPathway 0.005405 0.029215 0.142857 the 7

ST_IL_13_PATHWAY Like IL-4, IL-13 is produced by Th2 cells on activation of 1 T cell antigen receptor, and by mast and ba

ChemicalGeneticPerturbations environmental stress response that were not regulated following treatment of f

4NQO_ESR_OLD_UNREG 0.007714

Genes involved in the 0.038484 0.1 1 10

CanonicalPathway

B 0.007714 0.038484 0.1 1 10

BLYMPHOCYTEPATHWAYcells express the major histocompatibility complex (class II MHC), immunoglobulins, adhesion protei

CanonicalPathway 0.006175 0.031859 0.125 1 8

NEUTROPHILPATHWAYNeutrophils are phagocytotic leukocytes that destroy foreign cells with reactive oxygen species or enz

C na

module_424 ancerModules 8.45E-05 0.001009 0.111111 2 18

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

TGFBETA_C2_UP 1.11E-04 0.016759 of skin fibroblasts, cluster 2 18

Upregulated by TGF-beta treatment0.111111 2

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

Oligodendroglia/myelination

5.69E-05 0.009214 0.125 2 16

ASTON_OLIGODENDROGLIA_MYELINATION_SUBSETrelated genes which are downregulated in major depressive disorder (p <

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway functions as a second messenger activating the4

CACAMPATHWAY Calcium 5.81E-06 0.001107 0.333333 12

calcium/calmodulin-dependent kinases, which

ChemicalGeneticPerturbations

Upregulated by sulindac 0.041344 in0.105263

HDACI_COLON_SUL16HRS_UP 4

6.98E-04 at 16 hrs SW260 colon carcinoma cells 38

CanonicalPathway is expressed in skeletal muscle, heart muscle, and brown fat, and is a coactivator for receptors

PGC1APATHWAY PCG-1a 6.52E-05 0.0079 0.190476 4 21

ChemicalGeneticPerturbations

Down-regulated

4.29E-05 0.005722 0.210526 4 19

CMV_HCMV_TIMECOURSE_18HRS_DN in fibroblasts following infection with human cytomegalovirus (at least 3-fold, with Af

ChemicalGeneticPerturbations

IL6_FIBRO_UP 1.13E-04 0.010422 0.111111 5

Upregulated following IL-6 treatment in normal skin fibroblasts 45

GOBiologicalProcess

Genes annotated by the 0.001035 GO:0019933. A series7 molecular signals in which a cell uses cyclic

CAMP_MEDIATED_SIGNALING 5.82E-06 GO term 0.107692 of 65

GNF2_RAB3A na

CancerGeneNeighborhood 4.53E-04 0.029474 0.117647 4 34

GOCellularComponent 3.16E-04 0.022169 GO:0044456. The junction between a nerve fiber of one neuron and

SYNAPSE_PART Genes annotated by the GO term 0.230769 3 13

C na

module_533 ancerModules 8.50E-04 0.046236 0.1 4 40

GNF2_DNM1 na

CancerGeneNeighborhood 3.02E-09 1.34E-06 0.144928 10 69

CancerGeneNeighborhood

GNF2_TM4SF2 na 7.90E-05 0.008777 0.181818 4 22

CanonicalPathway

NDKDYNAMINPATHWAY 6.04E-04 Phosphins 0.1875

Endocytotic role of NDK,0.036614 and Dynamin 3 16

GOBiologicalProcess

Genes annotated by the 0.001075 GO:0007188. The series of molecular signals generated as a consequ

5.24E-06 GO term 0.109375

G_PROTEIN_SIGNALING__COUPLED_TO_CAMP_NUCLEOTIDE_SECOND_MESSENGER 7 64

CanonicalPathway coupled receptors activate adenylyl cyclase, which converts ATP to cAMP, to activate second

GPCRPATHWAY G-protein 3.15E-04 0.022719 0.129032 4 31

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

Oligodendroglia/myelination

6.63E-05 0.021091 0.125 2 16

ASTON_OLIGODENDROGLIA_MYELINATION_SUBSETrelated genes which are downregulated in major depressive disorder (p <

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations cancer cell lines reistant to doxorubicin, compared to parent chemosensitive lin

DOX_RESIST_GASTRIC_UP 9.06E-11

Upregulated in gastric 1.77E-08 0.125 5 40

ChemicalGeneticPerturbations

Coregulated and trans-regulated putative downstream targets of the cis-regulated HSC transcript, Fli1

BYSTRYKH_FLI1_TARGETS_GLOCUS 0.006945 0.028887 0.111111 1 9

GOMolecularFunction 0.007714 0.031093 GO:0048487. Interacting selectively with the microtubule constituen

BETA_TUBULIN_BINDING Genes annotated by the GO term 0.1 1 10

CanonicalPathway

SRCRPTPPATHWAY Src by Protein-tyrosine 0.1

Activation of0.007714 0.031093 phosphatase alpha1 10

chr16p Positional na 0.003092 0.015113 0.25 1 4

ChemicalGeneticPerturbationsDAC treatment in LD419 fibroblast cells

DAC_FIBRO_DN 0.007714 0.031093

Downregulated by 0.1 1 10

ChemicalGeneticPerturbations

9.06E-09 1.18E-06 0.121212 4 33

GREENBAUM_E2A_UP Table includes transcripts up-regulated 3-fold or greater in the E2A-deficient cell lines

C na

GNF2_ESPL1 ancerGeneNeighborhood 1.16E-08 1.13E-06 0.114286 4 35

ChemicalGeneticPerturbationsH2O2, Menadione and t-BH in breast cancer cells

OXSTRESS_BREASTCA_DN 0.006945 0.028887 0.111111

Downregulated by 1 9

CanonicalPathway

PTC1PATHWAY 0.007714 0.031093 0.1 1 10

The binding of extracellular signaling protein Sonic hedgehog to the Patched receptor (Ptc1) allows pro

ChemicalGeneticPerturbations

3.65E-05 timepoints (4-8 hrs) 2 12

P21_P53_EARLY_DN Down-regulated at early 3.76E-04 0.166667 following ectopic expression of p21 (CDKN1A) in OvCa ce

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

chryq11 Positional na 1.11E-11 1.29E-09 0.233333 7 30

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

chryq11 Positional na 3.43E-07 3.30E-05 0.1 3 30

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

Oligodendroglia/myelination

2.63E-05 0.005524 0.125 2 16

ASTON_OLIGODENDROGLIA_MYELINATION_SUBSETrelated genes which are downregulated in major depressive disorder (p <

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway

NOS1PATHWAY 3.98E-05 0.005967 0.166667 3 18

Glutamate stimulates NMDA-mediates calcium influx, which promotes nitric oxide synthesis from argi

C na

GNF2_MAPTancerGeneNeighborhood 1.22E-05 0.002038 0.105263 4 38

GNF2_DNM1 na

CancerGeneNeighborhood 1.17E-10 8.75E-08 0.115942 8 69

GNF2_RAB3A na

CancerGeneNeighborhood 2.77E-09 1.04E-06 0.176471 6 34

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

chr2q23 Positional na 4.19E-05 0.008166 0.111111 2 18

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway

SRCRPTPPATHWAY Src by Protein-tyrosine 0.1

Activation of0.005515 0.023972 phosphatase alpha1 10

CanonicalPathwayactivates the cdc2/cyclin B complex to induce the G2/M transition.

SA_G2_AND_M_PHASES Cdc25 0.004414 0.020187 0.125 1 8

CanonicalPathway

CDC25PATHWAY 0.004965 0.022016 0.111111 1 9

The protein phosphatase Cdc25 is phosphorylated by Chk1 and activates Cdc2 to stimulate eukaryotic

CanonicalPathway

PTC1PATHWAY 0.005515 0.023972 0.1 1 10

The binding of extracellular signaling protein Sonic hedgehog to the Patched receptor (Ptc1) allows pro

chr6p Positional na 0.004414 0.020187 0.125 1 8

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GNF2_RTN1 na

CancerGeneNeighborhood 1.07E-07 1.38E-04 0.111111 5 45

GOCellularComponent

Genes annotated by the GO term 0.153846 2 13

ENDOPLASMIC_RETICULUM_LUMEN5.06E-04 0.023202 GO:0005788. The volume enclosed by the membranes of the endop

C na

GNF2_MAPTancerGeneNeighborhood 2.77E-06 0.001184 0.105263 4 38

GNF2_MKI67 na

CancerGeneNeighborhood 4.10E-05 0.003758 0.115385 3 26

GNF2_AF1Q na

CancerGeneNeighborhood 1.82E-05 0.00212 0.15 3 20

GOMolecularFunction 0.001098 0.039172 GO:0005254. Catalysis of facilitated diffusion of an chloride (by an e

Genes annotated by the GO term 0.105263

CHLORIDE_CHANNEL_ACTIVITY 2 19

GNF2_H2AFX na

CancerGeneNeighborhood 7.82E-07 5.02E-04 0.142857 4 28

GOMolecularFunction 0.001218 GO term

Genes 0.1 2 20

ANION_CHANNEL_ACTIVITY annotated by the 0.041165 GO:0005253. Catalysis of the energy-independent passage of anions

CancerGeneNeighborhood

GNF2_SMC2L1 na 6.35E-05 0.004797 0.1 3 30

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

The sets differentially down-regulated

GALE_FLT3ANDAPL_DN 19 probe6.87E-09 4.75E-08 0.176471 in FLT3 3 17

ITD+ samples

C na

module_144 ancerModules 0 0 0.5 4 8

CancerGeneNeighborhood

GNF2_INPP5D na 9.70E-11 2.01E-09 0.102564 4 39

C na

module_143 ancerModules 0 0 0.307692 4 13

C na

module_293 ancerModules 0 0 0.363636 4 11

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

chryq11 Positional na 4.14E-11 3.85E-09 0.133333 4 30

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GOBiologicalProcess

Genes annotated

4.31E-04 GO term 0.117647 2 17

REGULATION_OF_ACTION_POTENTIAL by the 0.024071 GO:0001508. Any process that modulates the frequency, rate or ext

ChemicalGeneticPerturbations

Oligodendroglia/myelination

1.89E-11 5.27E-09 0.5 8 16

ASTON_OLIGODENDROGLIA_MYELINATION_SUBSETrelated genes which are downregulated in major depressive disorder (p <

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway

AHSPPATHWAY 4.03E-07 1.94E-05 0.166667 2 12

Alpha-hemoglobin stabilizing protein (AHSP) prevents precitipation of hemoglobin alpha-subunits.

ChemicalGeneticPerturbations

Genes 9.95E-04 0.005968 0.111111 1 9

PASSERINI_COMPLEMENT associated with cellular adhesion that are differentially expressed in endothelial cells of pig aort

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway expression by T cells induces apoptosis in Fas-expressing, inactive B cells.

BBCELLPATHWAY Fas ligand 5.50E-07 1.10E-05 0.5 2 4

CanonicalPathwayrequire interaction with helper T cells to produce2antigen-specific immunoglobulins as a key ele

ASBCELLPATHWAY B cells 2.56E-06 3.66E-05 0.25 8

Genes differentially

1.56E-05 7.45E-05 0.105263 2 19

DAVIES_N ChemicalGeneticPerturbations expressed in monoclonal gammopathy of uncertain significance (MGUS, a precurs

IL5PATHWAY Pro-inflammatory IL-5 is secretes by activated T cells, eosinophils, 10 mast cells, and stimulates the p

CanonicalPathway 4.12E-06 4.58E-05 0.2 2 and

CanonicalPathway T subtype Th1 produces pro-inflammatory cytokines that stimulate phagocytosis, while Th2 cel

TH1TH2PATHWAY Helper 1.24E-05 6.55E-05 0.117647 2 17

CanonicalPathway

TCRAPATHWAY 5.04E-06 4.58E-05 0.181818 T 11

The kinases Lck and Fyn phosphorylate and activate the2 cell receptor, which recognizes antigen-boun

CanonicalPathway

CTLA4PATHWAY 1.40E-05 interaction with an antigen-MHC-I complex on an antigen-presenting cell (AP

T cell activation requires 7.00E-05 0.111111 2 18

CanonicalPathway

B 4.12E-06 histocompatibility complex (class II MHC), immunoglobulins, adhesion protei

BLYMPHOCYTEPATHWAYcells express the major4.58E-05 0.2 2 10

CanonicalPathway

EOSINOPHILSPATHWAY 2.56E-06 3.66E-05 0.25 2 in

Recruitment of eosinophils in the inflammatory response observed8 asthma occurs via the chemoatt

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GNF2_MKI67 na

CancerGeneNeighborhood 5.26E-08 1.12E-05 0.115385 3 26

ChemicalGeneticPerturbationsDAC treatment in LD419 fibroblast cells

DAC_FIBRO_DN 4.12E-06 9.75E-05

Downregulated by 0.2 2 10

ChemicalGeneticPerturbationsH2O2, Menadione and t-BH in breast cancer cells

OXSTRESS_BREASTCA_DN 0.002982 0.014113 0.111111

Downregulated by 1 9

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

The sets differentially down-regulated

GALE_FLT3ANDAPL_DN 19 probe4.98E-06 9.71E-05 0.117647 in FLT3 2 17

ITD+ samples

C na

module_144 ancerModules 1.03E-06 8.00E-05 0.25 2 8

C na

module_143 ancerModules 2.86E-06 7.43E-05 0.153846 2 13

C na

module_293 ancerModules 2.02E-06 7.86E-05 0.181818 2 11

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

GOBiologicalProcess

Genes annotated by the GO term 0.1 1 10

HETEROPHILIC_CELL_ADHESION 0.003312 0.047348 GO:0007157. The attachment of an adhesion molecule in one cell to

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

CanonicalPathway of Neurotransmitter Relase by Botulinum Toxin

BOTULINPATHWAY Blockade 0.001381 0.036988 0.2 1 5

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

Genes highly0.001547 in hepatocellular carcinoma sensitive to 5-Fluorouracil + interferon.

expressed 0.008508 0.142857

KUROKAWA_5FU_IFN_SENSITIVE_VS_RESISTANT_UP 1 7

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

6.24E-11 9.23E-10 0.162162 of 37

ADIP_DIFF_CLUSTER5 Strongly upregulated at 24 hours during differentiation 6 3T3-L1 fibroblasts into adipocytes (cluster 5

GNF2_CDC2 na

CancerGeneNeighborhood 2.43E-11 4.45E-10 0.236364 13 55

CanonicalPathwaya transcription factor that promotes the G1/S transition, is repressed by Rb and activated by cd

SKP2E2FPATHWAY E2F-1, 0.015811 0.046237 0.111111 1 9

GOBiologicalProcess

Genes annotated by the GO term

3.58E-04 0.125

MITOTIC_SISTER_CHROMATID_SEGREGATION 0.001598 GO:0000070. The cell 2 16

cycle process whereby replicated homologous

ChemicalGeneticPerturbations 0

Genes upregulated 0 0.16129 10

SHEPARD_GENES_COMMON_BW_CB_MOin both the crb mutant and bymb morpholino in zebra fish 62

PTC1PATHWAY The binding of extracellular signaling protein Sonic hedgehog to the Patched receptor (Ptc1) allows pro

CanonicalPathway 1.35E-04 6.72E-04 0.2 2 10

ChemicalGeneticPerturbations

Genes 4.29E-10 multiple 0.217391 5 23

CROONQUIST_IL6_RAS_DN dowmregulated in5.75E-09 myeloma cells exposed to the pro-proliferative cytokine IL-6 versus

GNF2_CCNB2 na

CancerGeneNeighborhood 2.73E-12 1.12E-10 0.288462 15 52

ChemicalGeneticPerturbations

Genes 1.43E-05 8.57E-05 0.111111

GENOTOXINS_ALL_4HRS_REGregulated in mouse lymphocytes (TK 3.7.2C) at 4 3 27

hours by all six genotoxins tested (cisplatin, m

Genes annotated by the 4.21E-10 0.184211 7 38

SPINDLE GOCellularComponent 2.24E-11 GO term GO:0005819. The array of microtubules and associated molecules th

C na

GNF2_ESPL1 ancerGeneNeighborhood 1.84E-11 4.27E-10 0.2 7 35

ChemicalGeneticPerturbations

1.09E-06 timepoints hrs) 3 12

P21_P53_EARLY_DN Down-regulated at early 8.02E-06 (4-8 0.25 following ectopic expression of p21 (CDKN1A) in OvCa ce

GNF2_BUB1 na

CancerGeneNeighborhood 2.89E-11 4.91E-10 0.24 6 25

GNF2_MCM4 na

CancerGeneNeighborhood 2.18E-11 4.34E-10 0.18 9 50

MICROTUBULE Genes annotated by the 2.16E-06 0.129032 4 31

GOCellularComponent 2.45E-07 GO term GO:0005874. Any of the long, generally straight, hollow tubes of inte

KINETOCHORE Genes annotated by the 7.00E-05 0.12 3 25

GOCellularComponent 1.13E-05 GO term GO:0000776. A multisubunit complex that is located at the pericentr

GOBiologicalProcess

Genes annotated by the 6.28E-06 0.272727

8.22E-07 3 11

SPINDLE_ORGANIZATION_AND_BIOGENESIS GO term GO:0007051. A process that is carried out at the cellular level which

GNF2_MKI67 na

CancerGeneNeighborhood 9.81E-12 3.41E-10 0.346154 9 26

C na

module_451 ancerModules 2.45E-07 2.16E-06 0.129032 4 31

C na

module_303 ancerModules 1.22E-09 1.54E-08 0.178571 5 28

C na

module_403 ancerModules 1.63E-08 1.66E-07 0.108696 5 46

CanonicalPathway

CDC25PATHWAY 0.015811 0.046237 0.111111 1 9

The protein phosphatase Cdc25 is phosphorylated by Chk1 and activates Cdc2 to stimulate eukaryotic

ChemicalGeneticPerturbationsDAC treatment in LD419 fibroblast cells

DAC_FIBRO_DN 5.98E-07 4.84E-06

Downregulated by 0.3 3 10

CYTOKINESIS Genes annotated by the 0.001418 GO:0000910. A cellular process 15

GOBiologicalProcess 3.14E-04 GO term 0.133333 2 resulting in the division of the cytopl

na

GNF2_TTK CancerGeneNeighborhood 1.82E-11 4.37E-10 0.314286 11 35

C The ATM 2.34E-04 recognizes 0.153846 2 13

RBPATHWAYanonicalPathway protein kinase 0.001084 DNA damage and blocks cell cycle progression by phosphorylating

GNF2_CCNA2 na

CancerGeneNeighborhood 0 0 0.258065 16 62

GNF2_HMMR na

CancerGeneNeighborhood 1.59E-11 4.26E-10 0.295455 13 44

GOMolecularFunction

Genes annotated by the 1.93E-05 0.1875 3 16

MICROTUBULE_MOTOR_ACTIVITY 2.77E-06 GO term GO:0003777. Catalysis of movement along a microtubule, coupled to

GNF2_PCNA na

CancerGeneNeighborhood 0 0 0.225806 14 62

P21_ANY_DN Down-regulated at

3.36E-09 3.96E-08 0.147059 5 34

ChemicalGeneticPerturbations any timepoint (4-24 hrs) follwing ectopic expression of p21 (CDKN1A) in OvCa cells

ChemicalGeneticPerturbations

MIDDLEAGE_DN 7.97E-09 8.67E-08 0.285714 4 14

Downregulated in fibroblasts from middle-age individuals, compared to young

GOMolecularFunction 1.60E-05 GO term GO:0003774. Catalysis of movement along a polymeric molecule suc

MOTOR_ACTIVITY Genes annotated by the 9.43E-05 0.107143 3 28

C na

module_253 ancerModules 6.54E-06 4.26E-05 0.142857 3 21

GOBiologicalProcess

Genes 7.04E-07 5.45E-06 0.1 4 40

REGULATION_OF_MITOSIS annotated by the GO term GO:0007088. Any process that modulates the frequency, rate or ext

ChemicalGeneticPerturbations intermediate timepoints (12-16 hrs) 3

P21_MIDDLE_DN 1.81E-06 1.28E-05 0.214286

Down-regulated at 14

follwing ectopic expression of p21 (CDKN1A) in

GOBiologicalProcess

CELL_DIVISION 4.05E-04 GO term 0.117647 2 17

Genes annotated by the 0.001786 GO:0051301. The processes resulting in the physical partitioning and

C na

module_315 ancerModules 5.43E-11 8.22E-10 0.333333 5 15

GOBiologicalProcess

Genes 9.92E-06 6.22E-05 0.125 3 24

ORGANELLE_LOCALIZATION annotated by the GO term GO:0051640. The processes by which an organelle is transported to,

na

GNF2_FEN1CancerGeneNeighborhood 2.18E-11 4.47E-10 0.2 10 50

GOBiologicalProcess

Genes annotated by the GO term

5.98E-07 4.84E-06 0.3 3 10

MITOTIC_SPINDLE_ORGANIZATION_AND_BIOGENESIS GO:0007052. A process that is carried out at the cellular level which

OLDAGE_DN Downregulated in fibroblasts from old individuals, compared to young

1.45E-08 1.51E-07 0.111111

ChemicalGeneticPerturbations 5 45

na

GNF2_CKS2CancerGeneNeighborhood 1.28E-11 3.88E-10 0.26087 12 46

GNF2_CDC20 na

CancerGeneNeighborhood 1.61E-11 4.14E-10 0.27451 14 51

GOBiologicalProcess

Genes annotated by the GO

3.36E-06 2.32E-05 0.176471 3 17

ESTABLISHMENT_OF_ORGANELLE_LOCALIZATION term GO:0051656. The directed movement of an organelle to a specific lo

GOBiologicalProcess

Genes annotated by the GO term 0.117647 2 17

SISTER_CHROMATID_SEGREGATION 4.05E-04 0.001786 GO:0000819. The process by which sister chromatids are organized a

ChemicalGeneticPerturbations cancer cell lines reistant to doxorubicin, compared to parent chemosensitive lin

DOX_RESIST_GASTRIC_UP 3.62E-11

Upregulated in gastric 5.86E-10 0.225 9 40

CanonicalPathway 8.69E-06 5.60E-05 0.130435 3 23

CELLCYCLEPATHWAY Cyclins interact with cyclin-dependent kinases to form active kinase complexes that regulate progressi

CancerGeneNeighborhood

GNF2_SMC4L1 na 0 0 0.155844 12 77

na

GNF2_RFC3CancerGeneNeighborhood 9.88E-11 1.43E-09 0.153846 6 39

na

GNF2_RFC4CancerGeneNeighborhood 3.66E-11 5.79E-10 0.12069 7 58

PARP_KO_DN Downregulated in MEF cells from PARP knockout mice 2

2.34E-04 0.001084 0.153846

ChemicalGeneticPerturbations 13

C na

MORF_BUB1ancerGeneNeighborhood 3.02E-10 4.21E-09 0.12 6 50

GNF2_BUB1B na

CancerGeneNeighborhood 1.42E-11 4.12E-10 0.152174 7 46

GNF2_H2AFX na

CancerGeneNeighborhood 2.53E-11 4.40E-10 0.285714 8 28

C na

module_320 ancerModules 4.78E-06 3.23E-05 0.157895 3 19

C na

GNF2_RRM1ancerGeneNeighborhood 0 0 0.182927 15 82

GOCellularComponent 1.45E-08 GO term GO:0005876. Any microtubule that is part of a mitotic or meiotic spi

SPINDLE_MICROTUBULE Genes annotated by the 1.53E-07 0.25 4 16

C na

GNF2_RRM2ancerGeneNeighborhood 2.07E-11 4.50E-10 0.27027 10 37

GOBiologicalProcess

Genes annotated by the GO term GO:0000226.

4.06E-07 3.37E-06 0.114286 4 35

MICROTUBULE_CYTOSKELETON_ORGANIZATION_AND_BIOGENESIS A process that is carried out at the cellular level which

GNF2_CENPF na

CancerGeneNeighborhood 2.43E-11 4.45E-10 0.272727 15 55

GNF2_CENPE na

CancerGeneNeighborhood 2.07E-11 4.50E-10 0.297297 11 37

ChemicalGeneticPerturbations involved in0 0.101266

BRENTANI_CELL_CYCLECancer related genes0 the cell cycle 8 79

ChemicalGeneticPerturbations 0 at 16-24 hours during differentiation of 3T3-L1 fibroblasts into adipocytes with I

IDX_TSA_UP_CLUSTER3 Strongly up-regulated 0 0.134831 12 89

ChemicalGeneticPerturbations

50 top ranked SAM-defined over-expressed genes in each subgroup

ZHAN_MM_CD138_PR_VS_REST 2.20E-11 4.26E-10 0.315789 12 38

ChemicalGeneticPerturbations early0.001084 0.153846 follwing ectopic expression of p21 (CDKN1A) in OvCa cell

P21_EARLY_DN 2.34E-04 timepoints (4-8 hrs)

Down-regulated at 2 13

CanonicalPathway

SRCRPTPPATHWAY Src by Protein-tyrosine 0.2

Activation of 1.35E-04 6.72E-04 phosphatase alpha2 10

CanonicalPathwayactivates the cdc2/cyclin B complex to induce the G2/M transition.

SA_G2_AND_M_PHASES Cdc25 0.014066 0.04166 0.125 1 8

ChemicalGeneticPerturbations

2.87E-09 3.44E-08 0.151515 5 33

GREENBAUM_E2A_UP Table includes transcripts up-regulated 3-fold or greater in the E2A-deficient cell lines

na

module_57CancerModules 5.76E-10 7.57E-09 0.107143 6 56

ChemicalGeneticPerturbations in multiple myeloma cells exposed to the pro-proliferative cytokine IL-6 versus tho

Genes upregulated

CROONQUIST_IL6_STARVE_UP 5.69E-12 2.20E-10 0.212121 7 33

CanonicalPathwayE interacts with cell0.04166

FBW7PATHWAY Cyclin 0.014066 0.125 to 8

cycle checkpoint kinase cdk2 1 allow transcription of genes required for S p

ChemicalGeneticPerturbations 0 both ITTP0and DP more than 3-fold, with average signal value differences of at

LEE_TCELLS3_UP Transcripts enriched in 0.189474 18 95

CancerGeneNeighborhood

GNF2_SMC2L1 na 1.64E-11 4.09E-10 0.3 9 30

GOCellularComponent 4.05E-04 0.001786 GO:0000922. Either of the ends 17 a spindle, where spindle microtub

SPINDLE_POLE Genes annotated by the GO term 0.117647 2 of

C na

module_196 ancerModules 8.69E-06 5.60E-05 0.130435 3 23

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set

ChemicalGeneticPerturbations

expressed 0.029132 0.111111 1 9

LIZUKA_G2_SM_G3 Genes highly0.002485 in poorly differentiated vs. moderately differentiated hepatocellular carcinom

Annotation DescriptionOriginal PValue

Gene Set Name Category EnrichmentFlagged Genes In Genes in Set

Adjusted PValue Ratio Total Set