Reactome: A Curated Pathway Database
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Reactome Publications

2014

Wu G, Dawson E, Duong A, Haw R and Stein L. ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. 3:146 F1000Research.

Jupe S, Jassal B, Williams M, and Wu G. A controlled vocabulary for pathway entities and events. bau060. Publisher.

Backman S, Kollara A, Haw R, Stein L, Brown TJ. Glucocorticoid-Induced Reversal of Interleukin-1β-Stimulated Inflammatory Gene Expression in Human Oviductal Cells. PLoS ONE 9(5). PubMed.

2013

Croft D, Fabregat Mundo A, Haw R, Milacic, M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L and D’Eustachio P. The Reactome pathway knowledgebase. Nucleic Acids Res. PubMed

Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D’Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D. Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. PubMed

Croft, D. Building models using reactome pathways as templates. Methods Mol Biol. 1021:273-83. PubMed

D’Eustachio, P. Pathway databases: making chemical and biological sense of the genomic data flood. Chem Biol. 20(5):629-35. PubMed

2012

Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D’Eustachio P and Stein L. Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome. Cancers. 4 (4), 1180-1211.  Publisher

Wu G and Stein L. A network module-based method for identifying cancer prognostic signatures. Genome Biol. 13(12):R112. PubMed

Kim Y, Ignatchenko V, Yao CQ, Kalatskaya I, Nyalwidhe JO, Lance RS, Gramolini AO, Troyer DA, Stein LD, Boutros PC, Medin JA, Semmes OJ, Drake RR, Kislinger T. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics. 11(12):1870-84. PubMed

Haw R and Stein L. Using the reactome database. Curr Protoc Bioinformatics. Chapter 8:Unit 8.7. PubMed

Reveiller M, Ghatak S, Toia L, Kalatskaya I, Stein L, D’Souza M, Zhou Z, Bandla S, Gooding WE, Godfrey TE, Peters JH. Bile exposure inhibits expression of squamous differentiation genes in human esophageal epithelial cells. Ann Surg. 255(6):1113-20. PubMed

Sprowl JA, Reed K, Armstrong SR, Lanner C, Guo B, Kalatskaya I, Stein L, Hembruff SL, Tam A, Parissenti AM. Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells. Breast Cancer Res. 14(1):R2. PubMed

2011

Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH,……….. Soranzo N. New gene functions in megakaryopoiesis and platelet formation. Nature. 480(7376):201-8. PubMed

Ndegwa N, Côté RG, Ovelleiro D, D’Eustachio P, Hermjakob H, Vizcaíno JA, Croft D. Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database (Oxford). bar047. PubMed

Haw RA, Croft D, Yung CK, Ndegwa N, D’Eustachio P, Hermjakob H, Stein LD. The Reactome BioMart. Database (Oxford). bar047. PubMed

Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D’Eustachio P, Smith B, Blake JA, Wu C. The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics. 12:371. PubMed

Haw R, Hermjakob H, D’Eustachio P, Stein L. Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics. 11(18):3598-613. PubMed

Ismail A, Bandla S, Reveiller M, Toia L, Zhou Z, Gooding WE, Kalatskaya I, Stein L, D’Souza M, Litle VR, Peters JH, Pennathur A, Luketich JD, Godfrey TE. Early G₁ cyclin-dependent kinases as prognostic markers and potential therapeutic targets in esophageal adenocarcinoma. Clin Cancer Res. 17(13):4513-22. PubMed

Sawey ET, Chanrion M, Cai C, Wu G, Zhang J, Zender L, Zhao A, Busuttil RW, Yee H, Stein L, French DM, Finn RS, Lowe SW, and Powers S. Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by oncogenomic screening. Cancer Cell. 19(3): 347-58. PubMed

Jassal B. Pathway annotation and analysis with Reactome: The solute carrier class of membrane transporters. Human Genomics. 5(4):310-5.PubMed

D’Eustachio P. Reactome knowledgebase of human biological pathways and processes. Methods Mol Biol. 694:49-61. PubMed

Gillespie M, Shamovsky V, D’Eustachio P. Human and chicken TLR pathways: manual curation and computer-based orthology analysis. Mammalian Genome. 22(1-2):130-8. PubMed

Croft D, O’Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D’Eustachio P, Stein L. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. (Database issue). D691-7. PubMed

Dall’olio GM, Jassal B, Montanucci L, Gagneux P, Bertranpetit J, Laayouni H. The annotation of the Asparagine N-linked Glycosylation pathway in the Reactome Database. Glycobiology. 21(11):1395-400. PubMed

2010

Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, ……. McCarthy MI. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet. 42(7): 579-89. PubMed

Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D’Eustachio P. The systematic annotation of the three main GPCR families in Reactome. Database (Oxford). baq018. PubMed

Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. (Web Server issue) 38:W78-83. PubMed

Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11(5):R53. PubMed

2009

Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D’Eustachio P. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37:D619-22. PubMed

2007

Vastrik I, D’Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Genome Biol. 8:R39. PubMed

Matthews L, D’Eustachio P, Gillespie M, Croft D, de Bono B, Gopinath G, Jassal B, Lewis S, Schmidt E, Vastrik I, Wu G, Birney E, Stein L. An Introduction to the Reactome Knowledgebase of Human Biological Pathways and Processes. Bioinformatics Primer, NCI/Nature Pathway Interaction Database. doi:10.1038/pid.2007.3.

2005

Joshi-Tope G, Gillespie M, Vastrik I, D’Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 1:D428-32. PubMed

2004

Stein LD. Using the Reactome database. Curr Protoc Bioinformatics. Chapter 8:Unit 8.7. PubMed

2003

Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D’Eustachio P, Jassal B, Lewis S, Wu G, Birney E, Stein L. The Genome Knowledgebase: a resource for biologists and bioinformaticists. Cold Spring Harb Symp Quant Biol. 68:237-43. PubMed