Cell Metabolism Worksheet - Excel by sgk24546

VIEWS: 0 PAGES: 15

More Info
									Supplementary File 2 for "From E-MAPs to module maps: dissecting quantitative genetic interactions using physical i
This file contains listings of all the annotations used for annotating modules in this study. This worksheet contains GO biologica

Annotation                                                                                            Size
35S primary transcript processing                                                                              4
actin cytoskeleton organization and biogenesis                                                                 9
actin filament organization                                                                                    8
actin filament-based process                                                                                  10
aging                                                                                                         12
alcohol metabolism                                                                                            14
amino acid biosynthesis                                                                                        4
amino acid metabolism                                                                                          8
anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolism                        4
autophagy                                                                                                      2
base-excision repair                                                                                          10
base-excision repair, AP site formation                                                                        3
beta-tubulin folding                                                                                           2
biological_process                                                                                           739
bipolar bud site selection                                                                                     4
bud site selection                                                                                             7
budding cell bud growth                                                                                        8
calcium ion homeostasis                                                                                        2
carbohydrate metabolism                                                                                       12
cation homeostasis                                                                                             7
cation transport                                                                                               2
cell adhesion                                                                                                  6
cell aging                                                                                                    12
cell budding                                                                                                  13
cell cycle                                                                                                   179
cell cycle arrest                                                                                              3
cell cycle arrest in response to pheromone                                                                     2
cell cycle checkpoint                                                                                         29
cell growth                                                                                                   14
cell ion homeostasis                                                                                          11
cell morphogenesis                                                                                            42
cell morphogenesis checkpoint                                                                                  2
cell surface receptor linked signal transduction                                                               4
cell wall mannoprotein biosynthesis                                                                            2
cell wall organization and biogenesis                                                                         12
cell wall organization and biogenesis (sensu Fungi)                                                            2
cell-cell adhesion                                                                                             4
chromatin assembly or disassembly                                                                             70
chromatin modification                                                                                       124
chromatin remodeling                                                                                          91
chromatin silencing                                                                                           54
chromatin silencing at rDNA                                                                                    7
chromatin silencing at silent mating-type cassette                                                            15
chromatin silencing at telomere                                                                               34
chromosome localization                                                                                        2
chromosome organization and biogenesis (sensu Eukaryota)                                                     207
chromosome segregation                                                                                        43
chronological cell aging                                                                                       2
conjugation with cellular fusion                                                         14
cyclin catabolism                                                                         2
cytokinesis                                                                               9
cytoskeleton organization and biogenesis                                                 38
deadenylation-dependent decapping                                                         4
dephosphorylation                                                                         6
di-, tri-valent inorganic cation transport                                                2
DNA catabolism                                                                           10
DNA damage checkpoint                                                                     7
DNA metabolism                                                                          295
DNA recombinase assembly                                                                  5
DNA recombination                                                                        71
DNA repair                                                                              113
DNA replication                                                                          58
DNA replication checkpoint                                                                4
DNA replication initiation                                                                7
DNA replication, synthesis of RNA primer                                                  3
DNA replication-independent nucleosome assembly                                           5
DNA strand elongation                                                                    17
DNA topological change                                                                    5
DNA unwinding during replication                                                          4
DNA-dependent DNA replication                                                            45
double-strand break repair                                                               38
double-strand break repair via break-induced replication                                  6
double-strand break repair via homologous recombination                                  16
double-strand break repair via nonhomologous end joining                                 18
double-strand break repair via single-strand annealing                                   11
double-strand break repair via single-strand annealing, removal of nonhomologous ends     2
double-strand break repair via synthesis-dependent strand annealing                      11
endocytosis                                                                              12
endosome transport                                                                        5
ER to Golgi vesicle-mediated transport                                                    5
ER-associated protein catabolism                                                          4
ergosterol biosynthesis                                                                   3
establishment and/or maintenance of cell polarity (sensu Fungi)                          16
establishment and/or maintenance of chromatin architecture                              143
establishment of cell polarity (sensu Fungi)                                             16
establishment of mitotic spindle orientation                                              6
establishment of protein localization                                                    23
exocytosis                                                                                3
fatty acid metabolism                                                                     5
fermentation                                                                              2
filamentous growth                                                                       17
flocculation via cell wall protein-carbohydrate interaction                               4
G1 phase of mitotic cell cycle                                                           11
G1/S transition of mitotic cell cycle                                                    22
G1/S-specific transcription in mitotic cell cycle                                         6
G1-specific transcription in mitotic cell cycle                                           9
G2/M transition of mitotic cell cycle                                                    13
gene conversion at mating-type locus                                                     13
glucan metabolism                                                                         2
gluconeogenesis                                                                           6
glucose metabolism                                               8
glycerophospholipid metabolism                                   2
glycogen metabolism                                              2
Golgi vesicle transport                                         10
G-protein coupled receptor protein signaling pathway             2
heteroduplex formation                                           3
hexose metabolism                                                9
histone acetylation                                             17
histone deacetylation                                           10
histone exchange                                                 7
histone methylation                                             17
histone ubiquitination                                           3
homologous chromosome segregation                                2
intracellular protein transport                                 22
intracellular signaling cascade                                 11
intracellular transport                                         64
intra-Golgi vesicle-mediated transport                           2
invasive growth (sensu Saccharomyces)                            7
ion transport                                                    3
karyogamy during conjugation with cellular fusion                4
lagging strand elongation                                       12
leading strand elongation                                       10
lipid biosynthesis                                               7
lipid metabolism                                                19
loss of chromatin silencing                                      3
loss of chromatin silencing during replicative cell aging        2
M phase of mitotic cell cycle                                   48
maintenance of fidelity during DNA-dependent DNA replication    20
mating type switching                                           15
meiosis                                                         79
meiosis I                                                       52
meiotic chromosome segregation                                   8
meiotic DNA double-strand break formation                        8
meiotic DNA double-strand break processing                       3
meiotic DNA recombinase assembly                                 5
meiotic gene conversion                                         21
meiotic joint molecule formation                                 2
meiotic mismatch repair                                          7
meiotic recombination                                           41
meiotic recombination checkpoint                                 2
meiotic sister chromatid segregation                             3
membrane fusion                                                  3
membrane organization and biogenesis                             7
metabolism                                                     553
metal ion homeostasis                                            4
metal ion transport                                              2
methionine metabolism                                            3
microtubule cytoskeleton organization and biogenesis            22
microtubule depolymerization                                     3
microtubule-based process                                       29
misfolded or incompletely synthesized protein catabolism         4
mismatch repair                                                 20
mitochondrial genome maintenance                                                       5
mitochondrial membrane organization and biogenesis                                     2
mitochondrial signaling pathway                                                        3
mitochondrial transport                                                                2
mitochondrion inheritance                                                              3
mitochondrion organization and biogenesis                                             12
mitosis                                                                               47
mitotic anaphase                                                                       4
mitotic anaphase B                                                                     4
mitotic cell cycle                                                                    95
mitotic checkpoint                                                                    10
mitotic metaphase/anaphase transition                                                  4
mitotic recombination                                                                 18
mitotic sister chromatid cohesion                                                     11
mitotic sister chromatid segregation                                                  24
mitotic spindle checkpoint                                                            10
mitotic spindle elongation                                                             3
mitotic spindle organization and biogenesis                                           12
mitotic spindle organization and biogenesis in nucleus                                 9
monosaccharide metabolism                                                              9
monovalent inorganic cation homeostasis                                                2
mRNA 3'-end processing                                                                 3
mRNA catabolism                                                                       16
mRNA catabolism, deadenylation-dependent decay                                         8
mRNA cleavage                                                                          3
mRNA export from nucleus                                                              17
mRNA metabolism                                                                       27
mRNA polyadenylation                                                                   2
mRNA processing                                                                       13
mRNA-binding (hnRNP) protein import into nucleus                                       2
mutagenesis                                                                            7
negative regulation of DNA recombination                                               9
negative regulation of DNA replication                                                 4
negative regulation of DNA transposition                                               8
negative regulation of gluconeogenesis                                                 6
negative regulation of meiosis                                                         7
negative regulation of microtubule depolymerization                                    2
negative regulation of transcription                                                  69
negative regulation of transcription from RNA polymerase II promoter                  20
negative regulation of transcription from RNA polymerase II promoter by pheromones     2
negative regulation of transcription from RNA polymerase II promoter, mitotic          4
negative regulation of transcription, DNA-dependent                                   69
negative regulation of transcription, mitotic                                          5
nitrogen compound metabolism                                                          11
nitrogen utilization                                                                   2
NLS-bearing substrate import into nucleus                                              2
nuclear migration                                                                     11
nuclear migration, microtubule-mediated                                                9
nuclear mRNA splicing, via spliceosome                                                 9
nuclear organization and biogenesis                                                    6
nuclear pore organization and biogenesis                                               2
nucleobase, nucleoside, nucleotide and nucleic acid metabolism                       420
nucleocytoplasmic transport                                             24
nucleosome assembly                                                     10
nucleotide-excision repair                                              26
nucleotide-excision repair, DNA damage recognition                       7
nucleotide-excision repair, DNA duplex unwinding                         4
nucleotide-excision repair, DNA incision, 5'-to lesion                   2
one-carbon compound metabolism                                          17
oxygen and reactive oxygen species metabolism                            4
peroxisome organization and biogenesis                                   4
phosphate metabolism                                                    28
phospholipid biosynthesis                                                2
phospholipid metabolism                                                  9
phosphorylation                                                         21
poly(A) tail shortening                                                  2
poly(A)+ mRNA export from nucleus                                        2
polyadenylation-dependent ncRNA catabolism                               2
positive regulation of DNA replication                                   2
positive regulation of enzyme activity                                   2
positive regulation of transcription                                    24
positive regulation of transcription by galactose                        2
positive regulation of transcription from RNA polymerase II promoter    17
positive regulation of transcription, DNA-dependent                     21
post-chaperonin tubulin folding pathway                                  3
post-Golgi vesicle-mediated transport                                    2
postreplication repair                                                  10
premeiotic DNA synthesis                                                 4
processing of 27S pre-rRNA                                               2
proteasomal ubiquitin-dependent protein catabolism                      11
proteasome assembly                                                      2
protein amino acid acetylation                                          18
protein amino acid deacetylation                                        12
protein amino acid dephosphorylation                                     5
protein amino acid glycosylation                                         4
protein amino acid phosphorylation                                      20
protein biosynthesis                                                    18
protein catabolism                                                      31
protein complex assembly                                                25
protein deubiquitination                                                13
protein export from nucleus                                              4
protein folding                                                         14
protein import into nucleus                                              4
protein localization                                                    25
protein metabolism                                                     191
protein modification                                                   134
protein monoubiquitination                                              16
protein neddylation                                                      3
protein polyubiquitination                                              15
protein sumoylation                                                      4
protein targeting                                                       20
protein targeting to membrane                                            2
protein targeting to mitochondrion                                       2
protein targeting to vacuole                                             9
protein transport                                                       22
protein ubiquitination                                                  23
protein ubiquitination during ubiquitin-dependent protein catabolism     2
proteolysis                                                             26
pseudohyphal growth                                                      8
pyruvate metabolism                                                      8
Ras protein signal transduction                                          4
recombinational repair                                                  18
regulation of carbohydrate metabolism                                    8
regulation of catalytic activity                                        14
regulation of cell redox homeostasis                                     2
regulation of cell size                                                 25
regulation of cellular pH                                                2
regulation of cyclin-dependent protein kinase activity                  12
regulation of DNA recombination                                         11
regulation of DNA replication                                            8
regulation of DNA replication initiation                                 4
regulation of exit from mitosis                                          4
regulation of growth                                                     2
regulation of meiosis                                                   12
regulation of microtubule polymerization or depolymerization             2
regulation of mitosis                                                   17
regulation of mitotic metaphase/anaphase transition                      2
regulation of mRNA stability                                             8
regulation of pH                                                         2
regulation of progression through cell cycle                            61
regulation of progression through mitotic cell cycle                     6
regulation of protein biosynthesis                                       7
regulation of protein catabolism                                         3
regulation of S phase of mitotic cell cycle                              2
regulation of transcription                                            136
regulation of transcription from RNA polymerase I promoter               4
regulation of transcription from RNA polymerase II promoter             76
regulation of transcription from RNA polymerase III promoter             6
regulation of transcription, DNA-dependent                             133
regulation of translation                                                7
regulation of translational elongation                                   2
removal of nonhomologous ends                                            4
replicative cell aging                                                   8
response to chemical stimulus                                           31
response to DNA damage stimulus                                        137
response to drug                                                         6
response to exogenous dsRNA                                              4
response to nutrient                                                     2
response to osmotic stress                                               7
response to oxidative stress                                             4
response to pheromone                                                    8
response to pheromone during conjugation with cellular fusion            5
response to salt stress                                                  2
response to stress                                                     162
response to temperature stimulus                                         2
response to unfolded protein                                             3
retrograde transport, endosome to Golgi                3
retrograde vesicle-mediated transport, Golgi to ER     3
ribosomal large subunit biogenesis                     3
ribosomal protein import into nucleus                  2
ribosome assembly                                      2
ribosome biogenesis                                   25
ribosome biogenesis and assembly                      27
RNA catabolism                                        18
RNA elongation                                        25
RNA elongation from RNA polymerase II promoter        23
RNA export from nucleus                               18
RNA localization                                      18
RNA metabolism                                        43
RNA processing                                        24
RNA splicing                                           9
rRNA export from nucleus                               2
rRNA metabolism                                        9
rRNA processing                                        8
S phase of mitotic cell cycle                          4
secondary metabolism                                   2
secretory pathway                                     14
serine family amino acid biosynthesis                  2
serine family amino acid metabolism                    3
short-chain fatty acid metabolism                      2
signal transduction                                   17
signal transduction during filamentous growth          2
sister chromatid cohesion                             17
small GTPase mediated signal transduction              7
snoRNA 3'-end processing                               2
snoRNA metabolism                                      6
snoRNA processing                                      3
snRNA export from nucleus                              2
snRNP protein import into nucleus                      2
sphingolipid metabolism                                3
spindle organization and biogenesis                   14
spindle orientation checkpoint                         3
spliceosome assembly                                   2
spore wall assembly (sensu Fungi)                      3
sporulation                                           18
sporulation (sensu Fungi)                             16
steroid metabolism                                     3
sterol biosynthesis                                    3
sterol metabolism                                      3
sulfur amino acid metabolism                           3
sulfur metabolism                                      3
synapsis                                               7
synaptonemal complex formation                         4
telomere maintenance                                  84
telomere maintenance via recombination                 7
telomere maintenance via telomerase                    6
transcription                                        208
transcription from RNA polymerase I promoter          13
transcription from RNA polymerase II promoter                                   127
transcription from RNA polymerase III promoter                                   18
transcription initiation                                                         23
transcription initiation from RNA polymerase II promoter                         21
transcription initiation from RNA polymerase III promoter                         2
transcription termination                                                         9
transcription termination from Pol II promoter, RNA polymerase(A) coupled         6
transcription termination from Pol II promoter, RNA polymerase(A)-independent     5
transcription termination from RNA polymerase II promoter                         8
transcription, DNA-dependent                                                    199
translation                                                                       8
translational elongation                                                          3
transport                                                                        78
traversing start control point of mitotic cell cycle                              2
tRNA export from nucleus                                                          2
tRNA modification                                                                 7
tRNA processing                                                                   2
tubulin folding                                                                   8
ubiquitin cycle                                                                  51
ubiquitin-dependent protein catabolism                                           25
vacuolar acidification                                                            2
vacuolar protein catabolism                                                       2
vacuolar transport                                                               13
vacuole organization and biogenesis                                               3
vesicle fusion                                                                    2
vesicle-mediated transport                                                       29
eractions using physical interactions"
sheet contains GO biological process annotations. MIPS complexes and SGD phenotypes appear in separate files
Annotation                                         Size
19/22S regulator                                           3
20S proteasome                                             2
26S proteasome                                             2
Actin-associated proteins                                  2
ADA complex                                                3
Anaphase promoting complex (APC)                           2
Casein kinase II                                           4
CCR4 complex                                               2
Cdc28p complexes                                           9
Chl4 protein complex                                       2
Chromatin assembly complex (CAC)                           3
Ctf19 protein complex                                      2
Ctf3 protein complex                                       3
Ddc1p-Mec3p complex                                        2
DNA ligase IV                                              2
DNA polymerase delta (III)                                 2
DNA polymerase zeta                                        2
Dynein-complex motorproteins                               2
Gim complexes                                              5
HAT B complex                                              2
HDB complex                                                3
Kinesin-related motorproteins                              5
Kornberg's mediator (SRB) complex                         13
Ku complex                                                 2
MBF complex                                                2
MRE11/RAD50/XRS2 complex                                   3
MSH2/MSH3 complex                                          3
MSH2/MSH6 complex                                          2
NEF1 complex                                               3
NEF2 complex                                               2
NEF3 complex                                               5
NEF4 complex                                               2
NOT complex                                                2
Nucleosomal protein complex                                7
other DNA repair complexes                                 5
Replication complex                                        4
Replication factor A complex                               2
Replication factor C complex                               4
RNA polymerase I                                           7
RNA polymerase II                                          5
RNA polymerase III                                         6
RSC complex (Remodel the structure of chromatin)           5
RTG complex                                                2
SAGA complex                                              11
SAGA-like complex (SLIK)                                   2
SBF complex                                                2
Sin3 complex                                               2
SNF1 complex                                               3
SPB associated proteins                                    5
Srb10p complex                                             4
SWI/SNF transcription activator complex                    4
Synaptonemal complex (SC)     3
TAFIIs                        8
TFIIF                         3
TFIIH                         4
Tubulin-associated proteins   6
Annotation
caffeine hypersensitive (Null)
caffeine sensitive (Null)
cold sensitive (Null)
decreased drug resistance (rapamycin) (Heterozygous systematic deletion)
decreased drug resistance (rapamycin) (Systematic deletion)
decreased drug resistance (wortmannin) (Systematic deletion)
decreased levels of chitin (Systematic deletion)
decreased metabolite accumulation (glycogen) (Homozygous systematic deletion)
decreased resistance to calcofluor white (Systematic deletion)
decreased Ty3 transposition (Other)
elongated telomeres (Null)
Exhibits growth defect on a fermentable carbon source. (Systematic deletion)
exhibits growth defect on a non-fermentable (respiratory) carbon source (Systematic deletion)
Exhibits sensitivity at 15 generations when grown in 10 uM nystatin. (Systematic deletion)
Exhibits sensitivity at 15 generations when grown in galactose. (Systematic deletion)
Exhibits sensitivity at 15 generations when grown in medium of pH 8. (Systematic deletion)
Exhibits sensitivity at 15 generations when grown in minimal +his/leu/ura medium. (Systematic deletion)
Exhibits sensitivity at 20 generations when grown in 1 M NaCl. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in 1 M NaCl. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in 10 uM nystatin. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in galactose. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in medium of pH 8. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in minimal +his/leu/ura medium. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in synthetic complete - lys medium. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in synthetic complete - thr medium. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in synthetic complete - trp medium. (Systematic deletion)
Exhibits sensitivity at 5 generations when grown in synthetic complete medium. (Systematic deletion)
global transcriptional misregulation (Null)
haploinsufficient in rich medium (YPD) (Heterozygous systematic deletion)
increased drug resistance (rapamycin) (Systematic deletion)
increased drug resistance (wortmannin) (Systematic deletion)
increased levels of chitin (Systematic deletion)
increased metabolite accumulation (glycogen) (Homozygous systematic deletion)
increased resistance to calcofluor white (Systematic deletion)
increased resistance to caspofungin (Null)
increased sensitivity to caspofungin (Null)
inviable (Null)
inviable (Synthetic/multiple)
inviable (Systematic deletion)
Methylmercury resistance (Overexpression)
normal chitin levels (Systematic deletion)
normal drug resistance (wortmannin) (Systematic deletion)
normal resistance to calcofluor white (Systematic deletion)
not required for IME1 induction (Null)
Null mutant is viable; exhibits decreased sensitivity to the anticancer drug, cisplatin (Systematic deletion)
petite-negative (Null)
reduced fitness in rich medium (YPD) (Homozygous systematic deletion)
reduced telomeric silencing (Null)
required for meiotic nuclear divisions (Null)
sensitive to anticancer drug cisplatin (Null)
sensitive to anticancer drug oxaliplatin (Null)
shortened telomeres (Null)
slow growth (Null)
sporulation defective (Null)
suppresses lethality of rad53 null mutation (Overexpression)
temperature sensitive (Null)
thermosensitive (Null)
Tn3 insertion mutant demonstrates hypersensitivity to the cell surface polymer perturbing agent calcofluor white (Other)
UV sensitive (Null)
viable (Null)
viable (Systematic deletion)
Size
         2
         2
         4
         2
        58
        32
         5
        44
        25
        13
         9
        63
        56
         3
         2
        21
         8
        16
         8
        19
         3
        23
         8
         4
         7
        14
        15
         4
        22
        32
        15
        18
        43
         2
         3
         3
        47
         2
        72
         2
        25
        43
        10
         2
         5
         3
       243
         3
         2
         3
         3
 32
  7
  7
  3
  4
  5
  2
  3
 99
649

								
To top