Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number. Wang et al. (2006). Cancer Res.

Source:  Pearson correlation with 231,830 interactions from GEO

Tags:  transcription factors;  cancer

Multiclass cancer diagnosis using tumor gene expression signatures. Ramaswamy et al. (2001). Proc Natl Acad Sci U S A.

Source:  Pearson correlation with 226,615 interactions from supplementary material

Tags:  cancer

Genomic analysis reveals few genetic alterations in pediatric acute myeloid leukemia. Radtke et al. (2009). Proc Natl Acad Sci U S A.

Source:  Pearson correlation with 377,767 interactions from GEO

Tags:  transcription factors;  nervous system;  cancer

Expression profiling of liposarcoma yields a multigene predictor of patient outcome and identifies genes that contribute to liposarcomagenesis. Gobble et al. (2011). Cancer Res.

Source:  Pearson correlation with 449,507 interactions from GEO

Tags:  apoptosis;  cell line;  cultured cells;  cancer;  transcription factors

Gene expression classifiers for relapse-free survival and minimal residual disease improve risk classification and outcome prediction in pediatric B-precursor acute lymphoblastic leukemia. Kang et al. (2010). Blood.

Source:  Pearson correlation with 549,783 interactions from GEO

Tags:  transcription factors;  lymphoma;  cancer

A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling. Hummel et al. (2006). N Engl J Med.

Source:  Pearson correlation with 466,765 interactions from GEO

Tags:  cancer

Gene signatures of progression and metastasis in renal cell cancer. Jones et al. (2005). Clin Cancer Res.

Source:  Pearson correlation with 365,428 interactions from GEO

Tags:  transcription factors;  disease;  cancer

Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Bild et al. (2006). Nature.

Note:  One of 3 datasets produced from this publication.

Source:  Pearson correlation with 254,105 interactions from GEO

Tags:  cultured cells;  signal transduction;  cancer;  epithelial cells;  cell line;  disease;  breast;  transcription factors;  breast cancer

Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis. Noble et al. (2008). Gut.

Source:  Pearson correlation with 603,016 interactions from GEO

The effect of insulin on expression of genes and biochemical pathways in human skeletal muscle. Wu et al. (2007). Endocrine.

Source:  Pearson correlation with 223,988 interactions from GEO

Tags:  transcription factors;  muscle;  cultured cells

Gene expression analysis of soft tissue sarcomas: characterization and reclassification of malignant fibrous histiocytoma. Nakayama et al. (2007). Mod Pathol.

Source:  Pearson correlation with 361,398 interactions from GEO

Tags:  transcription factors;  cancer

Tumor cell gene expression changes following short-term in vivo exposure to single agent chemotherapeutics are related to survival in multiple myeloma. Burington et al. (2008). Clin Cancer Res.

Source:  Pearson correlation with 266,464 interactions from GEO

Tags:  transcription factors;  time series;  cancer;  chemotherapy

Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells. Burczynski et al. (2006). J Mol Diagn.

Source:  Pearson correlation with 419,356 interactions from GEO

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults. Raue et al. (2012). J Appl Physiol.

Source:  Pearson correlation with 483,849 interactions from GEO

Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage. Rieger et al. (2004). Proc Natl Acad Sci U S A.

Source:  Pearson correlation with 220,846 interactions from GEO

Tags:  cultured cells;  cell line

Mucosal gene expression of antimicrobial peptides in inflammatory bowel disease before and after first infliximab treatment. Arijs et al. (2009). PLoS One.

Source:  Pearson correlation with 570,210 interactions from GEO

Tags:  immune system

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. Peng et al. (2009). BMC Genomics.

Source:  Pearson correlation with 349,954 interactions from GEO

Tags:  liver

Gene expression changes in the course of normal brain aging are sexually dimorphic. Berchtold et al. (2008). Proc Natl Acad Sci U S A.

Source:  Pearson correlation with 507,933 interactions from GEO

Tags:  aging;  brain

Gene expression profiling and response signatures associated with differential responses to infliximab treatment in ulcerative colitis. Toedter et al. (2011). Am J Gastroenterol.

Source:  Pearson correlation with 572,082 interactions from GEO

Tags:  signal transduction;  immune system

Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Perou et al. (1999). Proc Natl Acad Sci U S A.

Source:  Pearson correlation with 50,804 interactions from supplementary material

Tags:  cultured cells;  cancer;  epithelial cells;  signal transduction;  breast;  stromal cells;  transcription factors;  breast cancer

Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Johnson et al. (2003). Science.

Source:  Pearson correlation with 426,934 interactions from GEO

Tags:  cultured cells;  cell line

A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Schadt et al. (2004). Genome Biol.

Note:  Predicted transcript array

Source:  Pearson correlation with 60,454 interactions from GEO

Source:  Direct interaction with 171 interactions from iRefIndex

Source:  Direct interaction with 345 interactions from BioGRID

A human functional protein interaction network and its application to cancer data analysis. Wu et al. (2010). Genome Biol.

Source:  78,448 interactions from supplementary material

Tags:  transcription factors;  cancer

Source:  Direct interaction with 24,924 interactions from Pathway Commons

Source:  Direct interaction with 937 interactions from Pathway Commons

Source:  Direct interaction with 10,118 interactions from Pathway Commons

Source:  Direct interaction with 598 interactions from Pathway Commons

Source:  Direct interaction with 685 interactions from Pathway Commons

Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes. Behzadnia et al. (2007). EMBO J.

Source:  Direct interaction with 101 interactions from iRefIndex

Interaction and assembly of murine pre-replicative complex proteins in yeast and mouse cells. Kneissl et al. (2003). J Mol Biol.

Source:  Direct interaction with 83 interactions from iRefIndex

Tags:  cell proliferation;  transcription factors;  cultured cells;  cell line

Proteomics analysis identifies phosphorylation-dependent alpha-synuclein protein interactions. McFarland et al. (2008). Mol Cell Proteomics.

Source:  Direct interaction with 152 interactions from iRefIndex

Tags:  brain;  nervous system

Systematic analysis of human protein complexes identifies chromosome segregation proteins. Hutchins et al. (2010). Science.

Source:  Direct interaction with 141 interactions from iRefIndex

Tags:  cell proliferation;  nervous system;  localization

Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Jeronimo et al. (2007). Mol Cell.

Source:  Direct interaction with 660 interactions from iRefIndex

Tags:  cultured cells;  cell line

Self-assembling protein microarrays. Ramachandran et al. (2004). Science.

Source:  Direct interaction with 119 interactions from iRefIndex

A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Goudreault et al. (2009). Mol Cell Proteomics.

Source:  Direct interaction with 242 interactions from iRefIndex

Tags:  nervous system

A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Sato et al. (2004). Mol Cell.

Source:  Direct interaction with 235 interactions from iRefIndex

Tags:  transcription factors

Large-scale structural analysis of the classical human protein tyrosine phosphatome. Barr et al. (2009). Cell.

Source:  Direct interaction with 177 interactions from iRefIndex

Source:  Direct interaction with 385 interactions from iRefIndex

A quantitative protein interaction network for the ErbB receptors using protein microarrays. Jones et al. (2006). Nature.

Source:  Direct interaction with 139 interactions from iRefIndex

Tags:  cultured cells;  cell line

Defining the human deubiquitinating enzyme interaction landscape. Sowa et al. (2009). Cell.

Note:  One of 2 datasets produced from this publication.

Source:  Direct interaction with 1,511 interactions from BioGRID

Source:  Direct interaction with 41,955 interactions from iRefIndex

Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS2. Cannavo et al. (2007). J Biol Chem.

Source:  Direct interaction with 109 interactions from iRefIndex

Tags:  transcription factors;  cell line;  cultured cells;  cancer

Source:  Direct interaction with 28,821 interactions from BioGRID

Source:  Direct interaction with 12,700 interactions from iRefIndex

Source:  Direct interaction with 5,310 interactions from iRefIndex

Source:  Direct interaction with 637 interactions from iRefIndex

Source:  Direct interaction with 21,448 interactions from iRefIndex

RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers. de Hoog et al. (2004). Cell.

Source:  Direct interaction with 220 interactions from iRefIndex

Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. Svendsen et al. (2009). Cell.

Source:  Direct interaction with 233 interactions from iRefIndex

Tags:  transcription factors;  cultured cells;  cell line

Source:  Direct interaction with 13,341 interactions from iRefIndex

An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Glatter et al. (2009). Mol Syst Biol.

Source:  Direct interaction with 307 interactions from iRefIndex

Tags:  cultured cells;  cell line

High-throughput mapping of a dynamic signaling network in mammalian cells. Barrios-Rodiles et al. (2005). Science.

Source:  Direct interaction with 547 interactions from iRefIndex

Tags:  cell signalling;  cell line;  cancer;  epithelial cells;  signal transduction;  cultured cells;  transcription factors

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.

Note:  I2D predictions of protein protein interactions using Chen-Pawson-2009 Mus musculus data

Source:  Direct interaction with 30 interactions from I2D

A map of the interactome network of the metazoan C. elegans. Li et al. (2004). Science.

Note:  I2D predictions of protein protein interactions using Li-Vidal-2004 Caenorhabditis elegans data

Source:  Direct interaction with 567 interactions from I2D

BioGRID: a general repository for interaction datasets. Stark et al. (2006). Nucleic Acids Res.

Note:  I2D predictions of protein protein interactions using BioGRID Saccharomyces cerevisiae data

Source:  Direct interaction with 13,434 interactions from I2D

Comparative assessment of large-scale data sets of protein-protein interactions. von Mering et al. (2002). Nature.

Note:  I2D predictions of protein protein interactions using vonMering-Bork-2002 Saccharomyces cerevisiae data

Source:  Direct interaction with 1,196 interactions from I2D

A map of the interactome network of the metazoan C. elegans. Li et al. (2004). Science.

Note:  I2D predictions of protein protein interactions using Li-Vidal-2004 Caenorhabditis elegans data

Source:  Direct interaction with 15 interactions from I2D

Comparative assessment of large-scale data sets of protein-protein interactions. von Mering et al. (2002). Nature.

Note:  I2D predictions of protein protein interactions using vonMering-Bork-2002 Saccharomyces cerevisiae data

Source:  Direct interaction with 3,001 interactions from I2D

Comparative assessment of large-scale data sets of protein-protein interactions. von Mering et al. (2002). Nature.

Note:  I2D predictions of protein protein interactions using vonMering-Bork-2002 Saccharomyces cerevisiae data

Source:  Direct interaction with 16,074 interactions from I2D

A gene-coexpression network for global discovery of conserved genetic modules. Stuart et al. (2003). Science.

Source:  24,952 interactions from supplementary material

Tags:  cell proliferation;  cultured cells;  signal transduction;  cancer

High-quality binary protein interaction map of the yeast interactome network. Yu et al. (2008). Science.

Note:  I2D predictions of protein protein interactions using Yu Gold Standard Saccharomyces cerevisiae data

Source:  Direct interaction with 386 interactions from I2D

Tags:  transcription factors;  signal transduction

The IntAct molecular interaction database in 2010. Aranda et al. (2010). Nucleic Acids Res.

Note:  I2D predictions of protein protein interactions using IntAct Rattus norvegicus data

Source:  Direct interaction with 1,054 interactions from I2D

MINT: a Molecular INTeraction database. Zanzoni et al. (2002). FEBS Lett.

Note:  I2D predictions of protein protein interactions using MINT Mus musculus data

Source:  Direct interaction with 977 interactions from I2D

MINT: a Molecular INTeraction database. Zanzoni et al. (2002). FEBS Lett.

Note:  I2D predictions of protein protein interactions using MINT Rattus norvegicus data

Source:  Direct interaction with 574 interactions from I2D

The IntAct molecular interaction database in 2010. Aranda et al. (2010). Nucleic Acids Res.

Note:  I2D predictions of protein protein interactions using IntAct Mus musculus data

Source:  Direct interaction with 3,422 interactions from I2D

BioGRID: a general repository for interaction datasets. Stark et al. (2006). Nucleic Acids Res.

Note:  I2D predictions of protein protein interactions using BioGRID Mus musculus data

Source:  Direct interaction with 288 interactions from I2D

Ontological visualization of protein-protein interactions. Drabkin et al. (2005). BMC Bioinformatics.

Note:  I2D predictions of protein protein interactions using MGI Mus musculus data

Source:  Direct interaction with 724 interactions from I2D

A map of the interactome network of the metazoan C. elegans. Li et al. (2004). Science.

Note:  I2D predictions of protein protein interactions using Li-Vidal-2004 Caenorhabditis elegans data

Source:  Direct interaction with 103 interactions from I2D

The IntAct molecular interaction database in 2010. Aranda et al. (2010). Nucleic Acids Res.

Note:  I2D predictions of protein protein interactions using IntAct Drosophila melanogaster data

Source:  Direct interaction with 3,920 interactions from I2D

BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bader et al. (2000). Bioinformatics.

Note:  I2D predictions of protein protein interactions using BIND Rattus norvegicus data

Source:  Direct interaction with 556 interactions from I2D

Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Tewari et al. (2004). Mol Cell.

Note:  I2D predictions of protein protein interactions usingTewari-Vidal-2004 Caenorhabditis elegans data

Source:  Direct interaction with 18 interactions from I2D

Tags:  development;  cultured cells;  cell line;  signal transduction;  cell signalling;  transcription factors;  kidney

BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bader et al. (2000). Bioinformatics.

Note:  I2D predictions of protein protein interactions using BIND Saccharomyces cerevisiae data

Source:  Direct interaction with 1,543 interactions from I2D

MINT: a Molecular INTeraction database. Zanzoni et al. (2002). FEBS Lett.

Note:  I2D predictions of protein protein interactions using MINT Caenorhabditis elegans data

Source:  Direct interaction with 1,166 interactions from I2D

InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Lynn et al. (2008). Mol Syst Biol.

Note:  I2D predictions of protein protein interactions using INNATEDB Mus musculus data

Source:  Direct interaction with 1,455 interactions from I2D

Tags:  signal transduction;  immune system

BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bader et al. (2000). Bioinformatics.

Note:  I2D predictions of protein protein interactions using BIND Caenorhabditis elegans data

Source:  Direct interaction with 911 interactions from I2D

An in vivo map of the yeast protein interactome. Tarassov et al. (2008). Science.

Note:  I2D predictions of protein protein interactions using Tarassov-Michnick-2008 Saccharomyces cerevisiae data

Source:  Direct interaction with 441 interactions from I2D

Tags:  cell proliferation

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Krogan et al. (2006). Nature.

Note:  I2D predictions of protein protein interactions using Krogan-Greenblatt-2006 Saccharomyces cerevisiae data

Source:  Direct interaction with 1,794 interactions from I2D

BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bader et al. (2000). Bioinformatics.

Note:  I2D predictions of protein protein interactions using BIND Mus musculus data

Source:  Direct interaction with 1,198 interactions from I2D

Source:  Pearson correlation with 530,357 interactions from Pfam

Source:  Pearson correlation with 488,822 interactions from InterPro