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Genome Res http://www.ncbi.nlm.nih.gov/pubmed/20923822 Co-expression Sheffer-Domany-2009 A 0.0001886780812391596 Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer. Sheffer et al. (2009). Proc Natl Acad Sci U S A http://www.ncbi.nlm.nih.gov/pubmed/19359472 Co-expression Swan-Spiller-2013 0.00018380083959175029 Identifying and testing candidate genetic polymorphisms in the irritable bowel syndrome (IBS): association with TNFSF15 and TNFα. Swan et al. (2013). Gut http://www.ncbi.nlm.nih.gov/pubmed/22684480 Co-expression Hessel-Tilley-2014 0.00014470462119401458 Intraflagellar transport gene expression associated with short cilia in smoking and COPD. Hessel et al. (2014). PLoS One http://www.ncbi.nlm.nih.gov/pubmed/24465567 Co-expression Wynn-Wong-2011 0.00013305369990066675 The influence of developmental age on the early transcriptomic response of children with septic shock. Wynn et al. (2011). Mol Med http://www.ncbi.nlm.nih.gov/pubmed/21738952 Co-expression Bjornsdottir-O'Toole-2011 0.0001327873548972682 Pathways activated during human asthma exacerbation as revealed by gene expression patterns in blood. Bjornsdottir et al. (2011). PLoS One http://www.ncbi.nlm.nih.gov/pubmed/21779351 Co-expression Miyake-Noguchi-2012 0.00013272104096987913 GSTP1 expression predicts poor pathological complete response to neoadjuvant chemotherapy in ER-negative breast cancer. Miyake et al. (2012). Cancer Sci http://www.ncbi.nlm.nih.gov/pubmed/22320227 Co-expression Dombroski-Spielman-2010 0.0001321795903690955 Gene expression and genetic variation in response to endoplasmic reticulum stress in human cells. Dombroski et al. (2010). Am J Hum Genet http://www.ncbi.nlm.nih.gov/pubmed/20398888 Co-expression Skov-Hasselbalch-2011 0.00012792317307871054 Whole-blood transcriptional profiling of interferon-inducible genes identifies highly upregulated IFI27 in primary myelofibrosis. Skov et al. 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PLoS One http://www.ncbi.nlm.nih.gov/pubmed/21364753 Co-expression Liu-Bratslavsky-2013 0.00009292162801152839 Impact of ischemia and procurement conditions on gene expression in renal cell carcinoma. Liu et al. (2013). Clin Cancer Res http://www.ncbi.nlm.nih.gov/pubmed/23136194 Co-expression Payton-Ley-2009 0.00009126838563684048 High throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples. Payton et al. (2009). J Clin Invest http://www.ncbi.nlm.nih.gov/pubmed/19451695 Co-expression Kohlmann-Haferlach-2008 B 0.00008551234026865726 An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase. Kohlmann et al. (2008). Br J Haematol http://www.ncbi.nlm.nih.gov/pubmed/18573112 Co-expression Klein-Dugas-2009 0.0000721419620269884 Quantitative comparison of microarray experiments with published leukemia related gene expression signatures. Klein et al. (2009). BMC Bioinformatics http://www.ncbi.nlm.nih.gov/pubmed/20003504 Co-expression Bild-Nevins-2006 C 0.0000664682783623442 Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Bild et al. (2006). Nature http://www.ncbi.nlm.nih.gov/pubmed/16273092 Co-expression Zangrando-Basso-2009 0.00006541731267575508 MLL rearrangements in pediatric acute lymphoblastic and myeloblastic leukemias: MLL specific and lineage specific signatures. Zangrando et al. (2009). BMC Med Genomics http://www.ncbi.nlm.nih.gov/pubmed/19549311 Co-expression Wong-Shanley-2009 A 0.00006288893919550733 Genomic expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum. Wong et al. (2009). Crit Care Med http://www.ncbi.nlm.nih.gov/pubmed/19325468 Co-expression Wong-Aronow-2007 0.0000557575954916018 Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome. Wong et al. (2007). Physiol Genomics http://www.ncbi.nlm.nih.gov/pubmed/17374846 Co-expression Driscoll-Munshi-2010 0.00003888041579529496 The sumoylation pathway is dysregulated in multiple myeloma and is associated with adverse patient outcome. Driscoll et al. (2010). Blood http://www.ncbi.nlm.nih.gov/pubmed/19965618 Co-expression Wong-Shanley-2009 B 0.00003846950421160876 Identification of pediatric septic shock subclasses based on genome-wide expression profiling. Wong et al. (2009). BMC Med http://www.ncbi.nlm.nih.gov/pubmed/19624809 Co-expression Suárez-Fariñas-Krueger-2012 0.000029625017835378274 Expanding the psoriasis disease profile: interrogation of the skin and serum of patients with moderate-to-severe psoriasis. Suárez-Fariñas et al. (2012). J Invest Dermatol http://www.ncbi.nlm.nih.gov/pubmed/22763790 Co-expression den Boon-Ahlquist-2015 0.000026595768639820024 Molecular transitions from papillomavirus infection to cervical precancer and cancer: Role of stromal estrogen receptor signaling. den Boon et al. (2015). Proc Natl Acad Sci U S A http://www.ncbi.nlm.nih.gov/pubmed/26056290 Co-expression Lenz-Staudt-2008 0.00001828377486806217 Stromal gene signatures in large-B-cell lymphomas. Lenz et al. (2008). N Engl J Med http://www.ncbi.nlm.nih.gov/pubmed/19038878 Co-expression Hanamura-Shaughnessy-2006 0.000009905431845117738 Prognostic value of cyclin D2 mRNA expression in newly diagnosed multiple myeloma treated with high-dose chemotherapy and tandem autologous stem cell transplantations. Hanamura et al. (2006). Leukemia http://www.ncbi.nlm.nih.gov/pubmed/16688228 Co-expression Ioannidis-Flaño-2012 0.000008092528551235279 Plasticity and virus specificity of the airway epithelial cell immune response during respiratory virus infection. Ioannidis et al. (2012). J Virol http://www.ncbi.nlm.nih.gov/pubmed/22398282 Co-expression Desmedt-Sotiriou-2007 0.0000018681210716389115 Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Desmedt et al. (2007). Clin Cancer Res http://www.ncbi.nlm.nih.gov/pubmed/17545524 Predicted I2D-vonMering-Bork-2002-High-Yeast2Human 0.007912509199584035 Comparative assessment of large-scale data sets of protein-protein interactions. von Mering et al. (2002). Nature http://www.ncbi.nlm.nih.gov/pubmed/12000970 Predicted I2D-vonMering-Bork-2002-Medium-Yeast2Human 0.005167116571909464 Comparative assessment of large-scale data sets of protein-protein interactions. von Mering et al. (2002). Nature http://www.ncbi.nlm.nih.gov/pubmed/12000970 Predicted I2D-BioGRID-Yeast2Human 0.004373750492654435 BioGRID: a general repository for interaction datasets. Stark et al. (2006). Nucleic Acids Res http://www.ncbi.nlm.nih.gov/pubmed/16381927 Predicted I2D-Chen-Pawson-2009-PiwiScreen-Mouse2Human 0.004096232857999004 Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Chen et al. (2009). Proc Natl Acad Sci U S A http://www.ncbi.nlm.nih.gov/pubmed/19918066 Predicted I2D-INNATEDB-Mouse2Human 0.0037587238122783325 InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Lynn et al. (2008). Mol Syst Biol http://www.ncbi.nlm.nih.gov/pubmed/18766178 Predicted I2D-Tarassov-PCA-Yeast2Human 0.0035614926461140944 An in vivo map of the yeast protein interactome. Tarassov et al. (2008). Science http://www.ncbi.nlm.nih.gov/pubmed/18467557 Predicted I2D-vonMering-Bork-2002-Low-Yeast2Human 0.003272642415822228 Comparative assessment of large-scale data sets of protein-protein interactions. von Mering et al. (2002). Nature http://www.ncbi.nlm.nih.gov/pubmed/12000970 Predicted Wu-Stein-2010 0.002909751813185715 A human functional protein interaction network and its application to cancer data analysis. Wu et al. (2010). Genome Biol http://www.ncbi.nlm.nih.gov/pubmed/20482850 Predicted I2D-IntAct-Mouse2Human 0.0027435642690487893 The IntAct molecular interaction database in 2010. Aranda et al. (2010). Nucleic Acids Res http://www.ncbi.nlm.nih.gov/pubmed/19850723 Predicted Stuart-Kim-2003 0.002281093861701329 A gene-coexpression network for global discovery of conserved genetic modules. Stuart et al. (2003). Science http://www.ncbi.nlm.nih.gov/pubmed/12934013 Predicted I2D-Yu-Vidal-2008-GoldStd-Yeast2Human 0.0019109473031592395 High-quality binary protein interaction map of the yeast interactome network. Yu et al. (2008). Science http://www.ncbi.nlm.nih.gov/pubmed/18719252 Predicted I2D-Krogan-Greenblatt-2006-Core-Yeast2Human 0.001718947943720029 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Krogan et al. (2006). Nature http://www.ncbi.nlm.nih.gov/pubmed/16554755 Predicted I2D-BIND-Rat2Human 0.0016829094619742406 BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bader et al. (2000). Bioinformatics http://www.ncbi.nlm.nih.gov/pubmed/10871269 Predicted I2D-BioGRID-Worm2Human 0.0016516865370825834 BioGRID: a general repository for interaction datasets. Stark et al. (2006). Nucleic Acids Res http://www.ncbi.nlm.nih.gov/pubmed/16381927 Predicted I2D-MINT-Rat2Human 0.0015009016798175985 MINT: a Molecular INTeraction database. Zanzoni et al. (2002). FEBS Lett http://www.ncbi.nlm.nih.gov/pubmed/11911893 Predicted I2D-MINT-Mouse2Human 0.001337865724651513 MINT: a Molecular INTeraction database. Zanzoni et al. (2002). FEBS Lett http://www.ncbi.nlm.nih.gov/pubmed/11911893 Predicted I2D-BIND-Mouse2Human 0.0012819816331155148 BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bader et al. (2000). Bioinformatics http://www.ncbi.nlm.nih.gov/pubmed/10871269 Predicted I2D-BioGRID-Mouse2Human 0.0010728201093370543 BioGRID: a general repository for interaction datasets. Stark et al. (2006). Nucleic Acids Res http://www.ncbi.nlm.nih.gov/pubmed/16381927 Predicted I2D-BIND-Yeast2Human 0.0010096264750674836 BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bader et al. (2000). Bioinformatics http://www.ncbi.nlm.nih.gov/pubmed/10871269 Predicted I2D-Krogan-Greenblatt-2006-NonCore-Yeast2Human 0.0007706146181831687 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Krogan et al. (2006). Nature http://www.ncbi.nlm.nih.gov/pubmed/16554755 Predicted I2D-IntAct-Fly2Human 0.0007655760648536147 The IntAct molecular interaction database in 2010. Aranda et al. (2010). Nucleic Acids Res http://www.ncbi.nlm.nih.gov/pubmed/19850723 Predicted I2D-Formstecher-Daviet-2005-Embryo-Fly2Human 0.0006694462897273705 Protein interaction mapping: a Drosophila case study. Formstecher et al. (2005). Genome Res http://www.ncbi.nlm.nih.gov/pubmed/15710747 Predicted I2D-MGI-Mouse2Human 0.0006026052638027231 Ontological visualization of protein-protein interactions. Drabkin et al. (2005). BMC Bioinformatics http://www.ncbi.nlm.nih.gov/pubmed/15707487 Predicted I2D-IntAct-Rat2Human 0.00007685077245695925 The IntAct molecular interaction database in 2010. Aranda et al. (2010). Nucleic Acids Res http://www.ncbi.nlm.nih.gov/pubmed/19850723 Predicted I2D-MINT-Worm2Human 0.000004936562885289321 MINT: a Molecular INTeraction database. Zanzoni et al. (2002). FEBS Lett http://www.ncbi.nlm.nih.gov/pubmed/11911893 Co-localization Zhang-Shang-2006 0.023133307634735412 The catalytic subunit of the proteasome is engaged in the entire process of estrogen receptor-regulated transcription. Zhang et al. (2006). EMBO J http://www.ncbi.nlm.nih.gov/pubmed/16957778 Co-localization Schadt-Shoemaker-2004 0.013784705343148232 A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Schadt et al. (2004). Genome Biol http://www.ncbi.nlm.nih.gov/pubmed/15461792 Co-localization Johnson-Shoemaker-2003 0.008578137022067294 Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Johnson et al. (2003). Science http://www.ncbi.nlm.nih.gov/pubmed/14684825 Co-localization Chen-Huang-2014 0.007347715696194343 Using an in situ proximity ligation assay to systematically profile endogenous protein-protein interactions in a pathway network. Chen et al. (2014). J Proteome Res http://www.ncbi.nlm.nih.gov/pubmed/25241761 Pathway Wu-Stein-2010 0.013632310370246209 A human functional protein interaction network and its application to cancer data analysis. Wu et al. (2010). Genome Biol http://www.ncbi.nlm.nih.gov/pubmed/20482850 Pathway REACTOME 0.011828008174151824 Pathway NCI_NATURE 0.0051521621665667145 Pathway CELL_MAP 0.004074667011485374 Pathway IMID 0.00370151646624114 Pathway HUMANCYC 0.00026023446895972454 Genetic Interactions Vizeacoumar-Moffat-2013 0.0036553365652002346 A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al. (2013). Mol Syst Biol http://www.ncbi.nlm.nih.gov/pubmed/24104479 Genetic Interactions BIOGRID-SMALL-SCALE-STUDIES 0.0034126614726264063 Genetic Interactions Toyoshima-Grandori-2012 0.0024431847052185833 Functional genomics identifies therapeutic targets for MYC-driven cancer. Toyoshima et al. (2012). Proc Natl Acad Sci U S A http://www.ncbi.nlm.nih.gov/pubmed/22623531 Genetic Interactions IREF-SMALL-SCALE-STUDIES 0.002035192876429895 Genetic Interactions Blomen-Brummelkamp-2015 0.0007096944709192212 Gene essentiality and synthetic lethality in haploid human cells. Blomen et al. (2015). Science http://www.ncbi.nlm.nih.gov/pubmed/26472760 Genetic Interactions Willingham-Muchowski-2003 0.00001880461814999316 Yeast genes that enhance the toxicity of a mutant huntingtin fragment or alpha-synuclein. Willingham et al. (2003). Science http://www.ncbi.nlm.nih.gov/pubmed/14657499 Shared protein domains INTERPRO 0.0033234024921137573 Shared protein domains PFAM 0.0018281180280980609