| Data type | Edge list download | #links | Description
|
|---|
| CC | download | 82319 | Inferred links by co-citation of two genes across 46,111 pubmed Medline article abstracts for yeast biology |
| CX | download | 242504 | Inferred links by co-expression pattern of two genes (based on high-dimensional gene expression data) |
| DC | download | 29880 | Inferred links by co-occurrence of protein domains between two coding genes |
| GN | download | 29475 | Inferred links by similar genomic context of bacterial orthologs of two yeast genes |
| GT | download | 149498 | Inferred links by similar profiles of genetic interaction partners |
| HT | download | 141347 | Links by high-throughput protein-protein interactions |
| LC | download | 54421 | Links by small/medium-scale protein-protein interactions (collected from protein-protein interaction data bases) |
| PG | download | 54496 | Inferred links by similar phylogenetic profiles between two yeast genes |
| TS | download | 3510 | Inferred links by 3-D protein structure of interacting orthologous proteins between two yeast proteins |
| DB/data set | Reference (PMID) | Edge list download | #links | Experiment description | New for v3?
|
|---|
| GSE1693 | 15899877 | download | 64519 | A novel response to microtubule perturbation in meiosis | Yes |
| GSE1934 | NA | download | 64520 | Ifh1 activates RP genes | Yes |
| GSE3076 | 17166056 | download | 26489 | Impact of Nonsense-mediated mRNA Decay on the Global Expression Profile of Budding Yeast | Yes |
| GSE7645 | NA | download | 33547 | Expression data for Saccharomyces cerevisiae oxidative stress response | Yes |
| GSE8799 | 18463633 | download | 23372 | Global Control of cell cycle transcription by coupled CDK and network oscillators | Yes |
| GSE9302 | 17043222 | download | 26774 | A perturbation in the system leads to period doubling | Yes |
| GSE10031 | 19235764 | download | 8514 | mRNA expression data in (delta)rsf1mutant during growth on, and transition to growth on glycerol as sole carbon source | Yes |
| GSE12220 | 18854817 | download | 24046 | Changes in Saccharomyces cerevisiae mRNA abundance following oxidative stress and DNA damage stress | Yes |
| GSE12221 | 18854817 | download | 26879 | Decay profiles of Saccharomyces cerevisiae mRNAs following oxidative stress and DNA damage | Yes |
| GSE12442 | 19804647 | download | 31911 | Transcriptional profile of Sacchromyces cerevisiae in different levels of oxygen provision | Yes |
| GSE13684 | 19158363 | download | 59245 | High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors | Yes |
| GSE14748 | NA | download | 14670 | Yeast genomic expression patterns in response to deoxynivalenol | Yes |
| GSE15254 | 20233714 | download | 27488 | Integration of the general amino acid control and nitrogen regulatory pathways in yeast nitrogen assimilation | Yes |
| GSE15936 | 19536156 | download | 19011 | Expression data from S. cerevisiae under serial stresses | Yes |
| GSE16799 | 19680226 | download | 13465 | Expression data for UV time course in Saccharomyces cerevisiae wild-type and mutant strains | Yes |
| GSE17364 | 20737431 | download | 28800 | Sodium arsenate response of wild type and slt2 deficient cells | Yes |
| GSE17716 | 22384390 | download | 14010 | Transcription data from Saccharomyces cerevisiae yeast | Yes |
| GSE17877 | NA | download | 8473 | Responses to inhibitors in an industrial strain of yeast and the adapted strains | Yes |
| GSE19016 | 20231268 | download | 7073 | The metabolic responce to iron deficiency in Saccharomyces cerevisiae | Yes |
| GSE19213 | 20971184 | download | 17433 | Expression data from oxidant treated yeast | Yes |
| GSE20108 | NA | download | 19952 | Responses to ethanol in haploid and diploid strain | Yes |
| GSE22269 | 20581845 | download | 41698 | Expression data from Saccharomyces cerevisiae treated with Small Molecule Enhancers of Rapamycin (SMERs) | Yes |
| GSE22832 | 21348598 | download | 18597 | Transcriptional response of Sacchromyces cerevisiae to change in oxygen provision | Yes |
| GSE23012 | NA | download | 32358 | Metabolic and transcriptional dynamics during the transition from carbon limitation to nitrogen limitation in Saccharomyces cerevisiae | Yes |
| GSE23204 | NA | download | 15508 | The Role of the Rad4-Rad23 Complex and Rad4 Ubiquitination in UV-Responsive Transcription | Yes |
| GSE24802 | 21701562 | download | 13718 | Expression data from Saccharomyces cerevisiae strains deleted for different subunits of the THO/TREX complex | Yes |
| GSE24888 | NA | download | 19708 | Phytochemical variations in medicinal herbs affecting bioefficacy: Equisetum arvense extracts in the global market place as a case study | Yes |
| GSE25582 | NA | download | 33470 | Time course expression data in wild-type and TF-deletion yeast | Yes |
| GSE26829 | 21931566 | download | 30790 | Measurements of mRNA abundance and decay for two strains 211 (wt) and 212 (mutant) | Yes |
| GSE26923 | 22558379 | download | 25122 | Expression data from S. cerevisiae, S288C with graded GCN5 F221A | Yes |
| GSE27062 | 22380681 | download | 37250 | Balancing Protein Folding and Disulfide Bond Formation Rates is Key to Mitigating Secretory Stress | Yes |
| GSE27234 | 21474073 | download | 36296 | Dot1 and Histone H3K79 Methylation in Natural Heterochromatic and HML/HMR Silencing | Yes |
| GSE27235 | NA | download | 40149 | Mutations in cohesin-associated genes impair protein translation | Yes |
| GSE30052 | 22289124 | download | 22124 | Dynamics of two oscillation phenotypes in S. cerevisiae [4hr] | Yes |
| GSE30054 | NA | download | 10931 | Genome wide transcriptional oscillation for Saccharomyces cerevisiae CEN.PK122 | Yes |
| GSE31774 | 21971086 | download | 11956 | Effect of loss of function of Gal11/Med15 and Med3 from the Mediator tail module in budding yeast | Yes |
| GSE32974 | 22306294 | download | 20342 | Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network | Yes |
| GSE33276 | NA | download | 18571 | Gene expression profiles of S. cerevisiae under heat stress | Yes |
| GSE33427 | 22745270 | download | 10973 | Genome-wide Response of Saccharomyces cerevisiae upon Arsenate Exposure | Yes |
| GSE34964 | 23001663 | download | 12004 | Transcriptomic analysis of the oxygen response in Saccharomyces cerevisiae EC1118 under wine fermentation conditions | Yes |
| GSE36954 | 22897823 | download | 12781 | Yeast genomic expression patterns in response to type B trichothecenes | Yes |
| GSE38848 | 23435897 | download | 14268 | Expression data from Saccharomyces cerevisiae | Yes |
| GSE40399 | NA | download | 23898 | Distinct Signaling Roles of Ceramide Species in Yeast Revealed Through Integromics Analyses | Yes |
| GSE40817 | 23197825 | download | 11055 | Expression data from S. cerevisiae after evolution under diverse conditions | Yes |
| SMD/Cellcycle | NA | download | 10702 | Cell cycle time course | No |
| SMD/Diauxic | NA | download | 19702 | Diauxic shift time course | No |
| SMD/DNAdamage | NA | download | 7955 | DNA damage time course | No |
| SMD/Nutrition | NA | download | 9092 | Starvation stress time course | No |
| SMD/Osmotic | NA | download | 41790 | Osmotic stress time course | No |
| SMD/YPDstat | NA | download | 7066 | Static growth in YPD media, time course | No |
| Reference (PMID) | Edge list download | #links | Experiment description | New for v3?
|
|---|
| 20093466 | download | 19413 | Synthetic genetic array (SGA) test for ~1700 query genes (Costanzo et al. Science 2010) | Yes |
| 20093466 | download | 43465 | Synthetic genetic array (SGA) test for ~3900 array genes (Costanzo et al. Science 2010) | Yes |
| 21987634 | download | 87492 | SGA test for 1487 query genes for mapping high-density genetic interactions among mitochondrial genes (Hoppins et al. J Cell Biol. 2011) | Yes |
| 21987634 | download | 21157 | SGA test for 481 array genes for mapping high-density genetic interactions among mitochondrial genes (Hoppins et al. J Cell Biol. 2011) | Yes |
| 21623372 | download | 9503 | SGA test for ~610 query genes x ~470 array genes for metabolic pathways (Szappanos et al. Nat. Genet 2011) | Yes |
| 16269340 | download | 209 | Epistatic miniarray profiles (E-MAP) for ~420 genes of early secretory pathway (Schuldiner et al. Cell 2005) | Yes |
| 17314980 | download | 51502 | E-MAP for ~740 genes of chromosome biology (Collins et al. Nature 2007) | Yes |
| 20526336 | download | 6495 | E-MAP for ~400 genes of plasma membrane biology including endocytosis, signaling, lipid metabolism, eisosome function (Aquilar et al. Nat. Struct. Mol. Biol. 2010) | Yes |
| 19269370 | download | 7496 | E-MAP for ~480 genes including all kinase, phosphatase, key cellular regulators (Fiedler et al. Cell 2009) | Yes |
| 20959818 | download | 13126 | E-MAP for ~150 specific TFs and ~170 general TFs (Zheng et al. Mol. Syst. Biol. 2010) | Yes |
| Reference (PMID) | Edge list download | #links | Experiment description | New for v3?
|
|---|
| 10688190 | download | 850 | Genome-scale yeast-two-hybrid (Y2H) screen (Uetz et al. Nature 2000) | No |
| 11283351 | download | 3908 | Genome-scale Y2H with pooled library (Ito et al. PNAS 2001) | No |
| 11805837 | download | 25549 | Genome-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 |
| 16429126 | download | 79431 | Genome-scale APMS (Gavin et al. Nature 2006) | No |
| 16554755 | download | 49992 | Genome-scale APMS with LCMS (Krogan et al. Nature 2006) | No |
| 16554755 | download | 41545 | Genome-scale APMS with MALDI (Krogan et al. Nature 2006) | No |
| 18719252 | download | 1546 | Genome-scale Y2H (Yu et al. Science 2008) | Yes |
| 20489023 | download | 18897 | Large-scale APMS for kinase and phosphatase interactions (Breitkreutz et al. Science 2010) | Yes |
| 22940862 | download | 50509 | Large-scale APMS for 1,590 membrane proteins (Babu et al. Nature 2012) | Yes |
| 21179020 | download | 2932 | Protein interactions for 102 chromatin-related proteins detected by modified chromatin immune-precipitation (mChIP-MS) (Lambert et al. Mol. Syst. Biol. 2010) | Yes |
| 18467557 | download | 2525 | Genome-wide protein-protein interactions by protein-fragment complementation assay (PCA) (Tarassov et al. Science 2008) | Yes |
| 14690591 | download | 688 | Interactome 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 |
