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Cell Metabolism Worksheet document sample
Document Sample
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
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