[YeastNet: a network by integration of all data-type-specific networks (CC, CX, DC, GN, GT, HT, LC PG, TS)]
YeastNet v.3
Edge list download5808 genes362421 links

[Gold standard data of positive gene functional associations]
YeastNet v.3-GS
Edge list download4172 genes81953 links

[Integrated networks for each of data types]
Data typeEdge list download#linksDescription
CCdownload82319Inferred links by co-citation of two genes across 46,111 pubmed Medline article abstracts for yeast biology
CXdownload242504Inferred links by co-expression pattern of two genes (based on high-dimensional gene expression data)
DCdownload29880Inferred links by co-occurrence of protein domains between two coding genes
GNdownload29475Inferred links by similar genomic context of bacterial orthologs of two yeast genes
GTdownload149498Inferred links by similar profiles of genetic interaction partners
HTdownload141347Links by high-throughput protein-protein interactions
LCdownload54421Links by small/medium-scale protein-protein interactions (collected from protein-protein interaction data bases)
PGdownload54496Inferred links by similar phylogenetic profiles between two yeast genes
TSdownload3510Inferred links by 3-D protein structure of interacting orthologous proteins between two yeast proteins

CX: networks by co-expression pattern between genes
DB/data setReference (PMID)Edge list download#linksExperiment descriptionNew for v3?
GSE169315899877download64519A novel response to microtubule perturbation in meiosisYes
GSE1934NAdownload64520Ifh1 activates RP genesYes
GSE307617166056download26489Impact of Nonsense-mediated mRNA Decay on the Global Expression Profile of Budding YeastYes
GSE7645NAdownload33547Expression data for Saccharomyces cerevisiae oxidative stress responseYes
GSE879918463633download23372Global Control of cell cycle transcription by coupled CDK and network oscillatorsYes
GSE930217043222download26774A perturbation in the system leads to period doubling Yes
GSE1003119235764download8514mRNA expression data in (delta)rsf1mutant during growth on, and transition to growth on glycerol as sole carbon source Yes
GSE1222018854817download24046Changes in Saccharomyces cerevisiae mRNA abundance following oxidative stress and DNA damage stressYes
GSE1222118854817download26879Decay profiles of Saccharomyces cerevisiae mRNAs following oxidative stress and DNA damageYes
GSE1244219804647download31911Transcriptional profile of Sacchromyces cerevisiae in different levels of oxygen provisionYes
GSE1368419158363download59245High-Resolution DNA Binding Specificity Analysis of Yeast Transcription FactorsYes
GSE14748NAdownload14670Yeast genomic expression patterns in response to deoxynivalenolYes
GSE1525420233714download27488Integration of the general amino acid control and nitrogen regulatory pathways in yeast nitrogen assimilationYes
GSE1593619536156download19011Expression data from S. cerevisiae under serial stressesYes
GSE1679919680226download13465Expression data for UV time course in Saccharomyces cerevisiae wild-type and mutant strainsYes
GSE1736420737431download28800Sodium arsenate response of wild type and slt2 deficient cellsYes
GSE1771622384390download14010Transcription data from Saccharomyces cerevisiae yeast Yes
GSE17877NAdownload8473Responses to inhibitors in an industrial strain of yeast and the adapted strainsYes
GSE1901620231268download7073The metabolic responce to iron deficiency in Saccharomyces cerevisiaeYes
GSE1921320971184download17433Expression data from oxidant treated yeast Yes
GSE20108NAdownload19952Responses to ethanol in haploid and diploid strainYes
GSE2226920581845download41698Expression data from Saccharomyces cerevisiae treated with Small Molecule Enhancers of Rapamycin (SMERs)Yes
GSE2283221348598download18597Transcriptional response of Sacchromyces cerevisiae to change in oxygen provisionYes
GSE23012NAdownload32358Metabolic and transcriptional dynamics during the transition from carbon limitation to nitrogen limitation in Saccharomyces cerevisiaeYes
GSE23204NAdownload15508The Role of the Rad4-Rad23 Complex and Rad4 Ubiquitination in UV-Responsive TranscriptionYes
GSE2480221701562download13718Expression data from Saccharomyces cerevisiae strains deleted for different subunits of the THO/TREX complexYes
GSE24888NAdownload19708Phytochemical variations in medicinal herbs affecting bioefficacy: Equisetum arvense extracts in the global market place as a case studyYes
GSE25582NAdownload33470Time course expression data in wild-type and TF-deletion yeastYes
GSE2682921931566download30790Measurements of mRNA abundance and decay for two strains 211 (wt) and 212 (mutant)Yes
GSE2692322558379download25122Expression data from S. cerevisiae, S288C with graded GCN5 F221AYes
GSE2706222380681download37250Balancing Protein Folding and Disulfide Bond Formation Rates is Key to Mitigating Secretory Stress Yes
GSE2723421474073download36296Dot1 and Histone H3K79 Methylation in Natural Heterochromatic and HML/HMR SilencingYes
GSE27235NAdownload40149Mutations in cohesin-associated genes impair protein translationYes
GSE3005222289124download22124Dynamics of two oscillation phenotypes in S. cerevisiae [4hr]Yes
GSE30054NAdownload10931Genome wide transcriptional oscillation for Saccharomyces cerevisiae CEN.PK122Yes
GSE3177421971086download11956Effect of loss of function of Gal11/Med15 and Med3 from the Mediator tail module in budding yeastYes
GSE3297422306294download20342Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor networkYes
GSE33276NAdownload18571Gene expression profiles of S. cerevisiae under heat stressYes
GSE3342722745270download10973Genome-wide Response of Saccharomyces cerevisiae upon Arsenate ExposureYes
GSE3496423001663download12004Transcriptomic analysis of the oxygen response in Saccharomyces cerevisiae EC1118 under wine fermentation conditionsYes
GSE3695422897823download12781Yeast genomic expression patterns in response to type B trichothecenesYes
GSE3884823435897download14268Expression data from Saccharomyces cerevisiaeYes
GSE40399NAdownload23898Distinct Signaling Roles of Ceramide Species in Yeast Revealed Through Integromics AnalysesYes
GSE4081723197825download11055Expression data from S. cerevisiae after evolution under diverse conditionsYes
SMD/CellcycleNAdownload10702Cell cycle time courseNo
SMD/DiauxicNAdownload19702Diauxic shift time courseNo
SMD/DNAdamageNAdownload7955DNA damage time courseNo
SMD/NutritionNAdownload9092Starvation stress time courseNo
SMD/OsmoticNAdownload41790Osmotic stress time courseNo
SMD/YPDstatNAdownload7066Static growth in YPD media, time courseNo

GT: networks by similarity of genetic interaction profiles between genes
Reference (PMID)Edge list download#linksExperiment descriptionNew for v3?
20093466download19413Synthetic genetic array (SGA) test for ~1700 query genes (Costanzo et al. Science 2010)Yes
20093466download43465Synthetic genetic array (SGA) test for ~3900 array genes (Costanzo et al. Science 2010)Yes
21987634download87492SGA test for 1487 query genes for mapping high-density genetic interactions among mitochondrial genes (Hoppins et al. J Cell Biol. 2011)Yes
21987634download21157SGA test for 481 array genes for mapping high-density genetic interactions among mitochondrial genes (Hoppins et al. J Cell Biol. 2011)Yes
21623372download9503SGA test for ~610 query genes x ~470 array genes for metabolic pathways (Szappanos et al. Nat. Genet 2011)Yes
16269340download209Epistatic miniarray profiles (E-MAP) for ~420 genes of early secretory pathway (Schuldiner et al. Cell 2005)Yes
17314980download51502E-MAP for ~740 genes of chromosome biology (Collins et al. Nature 2007)Yes
20526336download6495E-MAP for ~400 genes of plasma membrane biology including endocytosis, signaling, lipid metabolism, eisosome function (Aquilar et al. Nat. Struct. Mol. Biol. 2010)Yes
19269370download7496E-MAP for ~480 genes including all kinase, phosphatase, key cellular regulators (Fiedler et al. Cell 2009)Yes
20959818download13126E-MAP for ~150 specific TFs and ~170 general TFs (Zheng et al. Mol. Syst. Biol. 2010)Yes

HT: networks by high-throughput protein-protein interactions
Reference (PMID)Edge list download #linksExperiment descriptionNew for v3?
10688190download850Genome-scale yeast-two-hybrid (Y2H) screen (Uetz et al. Nature 2000) No
11283351download3908Genome-scale Y2H with pooled library (Ito et al. PNAS 2001) No
11805837download25549Genome-scale affinity purification followed by mass-spectrometry analysis of co-purified proteins (APMS) based on exogenously expressed bait proteins (Ho et al. Nature 2002). No
16429126download79431Genome-scale APMS (Gavin et al. Nature 2006) No
16554755download49992Genome-scale APMS with LCMS (Krogan et al. Nature 2006)No
16554755download41545Genome-scale APMS with MALDI (Krogan et al. Nature 2006)No
18719252download1546Genome-scale Y2H (Yu et al. Science 2008)Yes
20489023download18897Large-scale APMS for kinase and phosphatase interactions (Breitkreutz et al. Science 2010)Yes
22940862download50509Large-scale APMS for 1,590 membrane proteins (Babu et al. Nature 2012)Yes
21179020download2932Protein interactions for 102 chromatin-related proteins detected by modified chromatin immune-precipitation (mChIP-MS) (Lambert et al. Mol. Syst. Biol. 2010)Yes
18467557download2525Genome-wide protein-protein interactions by protein-fragment complementation assay (PCA) (Tarassov et al. Science 2008)Yes
14690591download688Interactome for 100 essential genes mapped by combination of 4 complementary methods (APMS, Y2H, split-YPD, structure based prediction) (Hazbun et al. Mol. Cell 2003)Yes

Back to Main