Enrichr: công cụ phân tích làm giàu danh sách gen HTML5 tương tác và hợp tác

Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37: 1-13. 10.1093/nar/gkn923.

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005, 102: 15545-15550. 10.1073/pnas.0506580102.

Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP: GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007, 23: 3251-3253. 10.1093/bioinformatics/btm369.

Smirnov N: Tables for estimating the goodness of fit of empirical distributions. Ann Math Stat. 1948, 19: 279-281. 10.1214/aoms/1177730256.

Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P: Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011, 27: 1739-1740. 10.1093/bioinformatics/btr260.

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H: Gene ontology: tool for the unification of biology. Nat Genet. 2000, 25: 25-10.1038/75556.

Fisher RA: On the interpretation of χ2 from contingency tables, and the calculation of P. J R Stat Soc. 1922, 85: 87-94. 10.2307/2340521.

Dannenfelser R, Clark N, Ma'ayan A: Genes2FANs: connecting genes through functional association networks. BMC Bioinforma. 2012, 13: 156-10.1186/1471-2105-13-156.

Clark N, Dannenfelser R, Tan C, Komosinski M, Ma'ayan A: Sets2Networks: network inference from repeated observations of sets. BMC Syst Biol. 2012, 6: 89-10.1186/1752-0509-6-89.

Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR: ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics. 2010, 26: 2438-2444. 10.1093/bioinformatics/btq466.

Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006, 34: D108-D110. 10.1093/nar/gkj143.

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X: JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010, 38: D105-D110. 10.1093/nar/gkp950.

Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ: The UCSC genome browser database: update 2007. Nucleic Acids Res. 2007, 35: D668-D673. 10.1093/nar/gkl928.

Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA: ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2012, 40: D912-D917. 10.1093/nar/gkr1012.

Consortium TEP: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489: 57-74. 10.1038/nature11247.

Chadwick LH: The NIH roadmap epigenomics program data resource. Epigenomics. 2012, 4: 317-324. 10.2217/epi.12.18.

Lewis BP, Burge CB, Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are MicroRNA targets. Cell. 2005, 120: 15-20. 10.1016/j.cell.2004.12.035.

Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH: Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics. 2012, 28: 105-111. 10.1093/bioinformatics/btr625.

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS: Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9: R137-10.1186/gb-2008-9-9-r137.

Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A: The NIH roadmap epigenomics mapping consortium. Nat Biotechnol. 2010, 28: 1045-1048. 10.1038/nbt1010-1045.

Zang C, Schones DE, Zeng C, Cui K, Zhao K: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009, 25: 1952-1958. 10.1093/bioinformatics/btp340.

Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009, 6: S22-S32. 10.1038/nmeth.1371.

Lewis BP, Shih I, Jones-Rhoades MW, Bartel DP, Burge CB: Prediction of mammalian microRNA targets. Cell. 2003, 115: 787-798. 10.1016/S0092-8674(03)01018-3.

Lachmann A, Ma'ayan A: Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinforma. 2010, 11: 87-10.1186/1471-2105-11-87.

Pico AR, Kelder T, Van Iersel MP, Hanspers K, Conklin BR: WikiPathways: pathway editing for the people. PLoS Biol. 2008, 6: e184-10.1371/journal.pbio.0060184.

Ogata H, Goto S, Fujibuchi W, Kanehisa M: Computation with the KEGG pathway database. Biosystems. 1998, 47: 119-128. 10.1016/S0303-2647(98)00017-3.

Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E: Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2005, 33: D428-D432.

Lachmann A, Ma'ayan A: KEA: kinase enrichment analysis. Bioinformatics. 2009, 25: 684-686. 10.1093/bioinformatics/btp026.

Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C: CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 2008, 36: D646-D650.

Malovannaya A, Lanz RB, Jung SY, Bulynko Y, Le NT: Analysis of the human endogenous coregulator complexome. Cell. 2011, 145: 787-799. 10.1016/j.cell.2011.05.006.

Graauw M, Pimienta G, Chaerkady R, Pandey A: SILAC for Global Phosphoproteomic Analysis. 2009, Phospho-Proteomics: Humana Press, 107-116.

Prasad TSK, Goel R, Kandasamy K, Keerthikumar S, Kumar S: Human protein reference database—2009 update. Nucleic Acids Res. 2009, 37: D767-D772. 10.1093/nar/gkn892.

Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B: PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics. 2004, 4: 1551-1561. 10.1002/pmic.200300772.

Yang CY, Chang CH, Yu YL, Lin TCE, Lee SA: PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. Bioinformatics. 2008, 24: i14-i20. 10.1093/bioinformatics/btn297.

Diella F, Cameron S, Gemünd C, Linding R, Via A: Phospho. ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinforma. 2004, 5: 79-10.1186/1471-2105-5-79.

Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K: NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 2008, 36: D695-D699.

Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M: MINT: a Molecular INTeraction database. FEBS Lett. 2002, 513: 135-140. 10.1016/S0014-5793(01)03293-8.

Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE: The mouse genome database genotypes: phenotypes. Nucleic Acids Res. 2009, 37: D712-D719. 10.1093/nar/gkn886.

Lamb J, Crawford ED, Peck D, Modell JW, Blat IC: The connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science Signalling. 2006, 313: 1929-

Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC: GeneSigDB—a curated database of gene expression signatures. Nucleic Acids Res. 2010, 38: D716-D725. 10.1093/nar/gkp1015.

Hamosh A, Scott AF, Amberger J, Valle D, McKusick VA: Online Mendelian inheritance in man (OMIM). Hum Mutat. 1999, 15: 57-61.

Chatr-aryamontri A, Ceol A, Peluso D, Nardozza A, Panni S: VirusMINT: a viral protein interaction database. Nucleic Acids Res. 2009, 37: D669-D673. 10.1093/nar/gkn739.

Berger SI, Posner JM, Ma'ayan A: Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinforma. 2007, 8: 372-10.1186/1471-2105-8-372.

Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004, 101: 6062-6067. 10.1073/pnas.0400782101.

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA: The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012, 483: 603-607. 10.1038/nature11003.

Weinstein JN: Spotlight on molecular profiling:“integromic†analysis of the NCI-60 cancer cell lines. Mol Cancer Ther. 2006, 5: 2601-2605. 10.1158/1535-7163.MCT-06-0640.

Wishart DS, Tzur D, Knox C, Eisner R, Guo AC: HMDB: the human metabolome database. Nucleic Acids Res. 2007, 35: D521-D526. 10.1093/nar/gkl923.

Bateman A, Coin L, Durbin R, Finn RD, Hollich V: The Pfam protein families database. Nucleic Acids Res. 2004, 32: D138-D141. 10.1093/nar/gkh121.

Apweiler R, Attwood TK, Bairoch A, Birney E, Biswas M: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001, 29: 37-40. 10.1093/nar/29.1.37.

Skellam J: Studies in statistical ecology: I Spatial pattern. Biometrika. 1952, 39: 346-362.

Clark PJ, Evans FC: Distance to nearest neighbor as a measure of spatial relationships in populations. Ecology. 1954, 35: 445-453. 10.2307/1931034.

Bostock M, Ogievetsky V, Heer J: D3 Data-Driven Documents. IEEE T Vis Comput Gr. 2011, 17: 2301-2309.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech. 2010, 28: 511-515. 10.1038/nbt.1621.

Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H: Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science. 2002, 298: 1039-1043. 10.1126/science.1076997.