{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T02:02:00Z","timestamp":1793412120207,"version":"4.5.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Identifying the cellular wiring that connects genomic perturbations to transcriptional changes in cancer is essential to gain a mechanistic understanding of disease initiation, progression and ultimately to predict drug response. We have developed a method called Tied Diffusion Through Interacting Events (TieDIE) that uses a network diffusion approach to connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The method computes a subnetwork of protein\u2013protein interactions, predicted transcription factor-to-target connections and curated interactions from literature that connects genomic and transcriptomic perturbations.<\/jats:p>\n                  <jats:p>Results: Application of TieDIE to The Cancer Genome Atlas and a breast cancer cell line dataset identified key signaling pathways, with examples impinging on MYC activity. Interlinking genes are predicted to correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor character and suggest subtype-specific drug targets.<\/jats:p>\n                  <jats:p>Availability: Software is available from the Stuart lab\u2019s wiki: https:\/\/sysbiowiki.soe.ucsc.edu\/tiedie.<\/jats:p>\n                  <jats:p>Contact: \u00a0jstuart@ucsc.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt471","type":"journal-article","created":{"date-parts":[[2013,8,28]],"date-time":"2013-08-28T20:29:04Z","timestamp":1377721744000},"page":"2757-2764","source":"Crossref","is-referenced-by-count":203,"title":["Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)"],"prefix":"10.1093","volume":"29","author":[{"given":"Evan O.","family":"Paull","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel E.","family":"Carlin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Niepel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter K.","family":"Sorger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Haussler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua M.","family":"Stuart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,8,27]]},"reference":[{"key":"2023063011062819500_btt471-B1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1126\/science.286.5439.509","article-title":"Emergence of scaling in random networks","volume":"286","author":"Barabasi","year":"1999","journal-title":"Science"},{"key":"2023063011062819500_btt471-B2","doi-asserted-by":"crossref","first-page":"20007","DOI":"10.1073\/pnas.0710052104","article-title":"Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma","volume":"104","author":"Beroukhim","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023063011062819500_btt471-B3","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1101\/gad.2017311","article-title":"Making sense of cancer genomic data","volume":"25","author":"Chin","year":"2011","journal-title":"Genes Dev."},{"key":"2023063011062819500_btt471-B4","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1101\/gr.125567.111","article-title":"Mutual exclusivity analysis identifies oncogenic network modules","volume":"22","author":"Ciriello","year":"2012","journal-title":"Genome Res."},{"key":"2023063011062819500_btt471-B5","doi-asserted-by":"crossref","first-page":"i223","DOI":"10.1093\/bioinformatics\/btn161","article-title":"Identifying functional modules in protein-protein interaction networks: an integrated exact approach","volume":"24","author":"Dittrich","year":"2008","journal-title":"Bioinformatics"},{"key":"2023063011062819500_btt471-B6","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkq929","article-title":"COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer","volume":"39","author":"Forbes","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023063011062819500_btt471-B7","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1006\/excr.1996.3457","article-title":"Overexpressed IGF-I receptors reduce estrogen growth requirements, enhance survival, and promote E-cadherin-mediated cell-cell adhesion in human breast cancer cells","volume":"231","author":"Guvakova","year":"1997","journal-title":"Exp. Cell Res."},{"key":"2023063011062819500_btt471-B8","doi-asserted-by":"crossref","first-page":"2724","DOI":"10.1073\/pnas.1018854108","article-title":"Subtype and pathway specific responses to anti-cancer compounds in breast cancer","volume":"21","author":"Heiser","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023063011062819500_btt471-B9","doi-asserted-by":"crossref","first-page":"ra40","DOI":"10.1126\/scisignal.2000350","article-title":"Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks","volume":"2","author":"Huang","year":"2009","journal-title":"Sci. Signal."},{"key":"2023063011062819500_btt471-B10","doi-asserted-by":"crossref","first-page":"D428","DOI":"10.1093\/nar\/gki072","article-title":"Reactome: a knowledgebase of biological pathways","volume":"33","author":"Joshi-Tope","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023063011062819500_btt471-B11","doi-asserted-by":"crossref","first-page":"D1301","DOI":"10.1093\/nar\/gkr1074","article-title":"WikiPathways: building research communities on biological pathways","volume":"40","author":"Kelder","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023063011062819500_btt471-B12","first-page":"504","article-title":"Master regulators used as breast cancer metastasis classifier","author":"Lim","year":"2009","journal-title":"Pac. Symp. Biocomput."},{"key":"2023063011062819500_btt471-B13","doi-asserted-by":"crossref","first-page":"5985","DOI":"10.1158\/0008-5472.CAN-06-0978","article-title":"Nuclear p21-activated kinase 1 in breast cancer packs off tamoxifen sensitivity","volume":"66","author":"Rayala","year":"2006","journal-title":"Cancer Res."},{"key":"2023063011062819500_btt471-B14","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the Pathway Interaction Database","volume":"37","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023063011062819500_btt471-B15","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023063011062819500_btt471-B16","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive molecular portraits of human breast tumours","volume":"490","author":"TCGA Network","year":"2012","journal-title":"Nature"},{"key":"2023063011062819500_btt471-B17","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"Tusher","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023063011062819500_btt471-B18","first-page":"55","article-title":"Discovery of mutated subnetworks associated with clinical data in cancer","author":"Vandin","year":"2012","journal-title":"Pac. Symp. Biocomput."},{"key":"2023063011062819500_btt471-B19","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1101\/gr.120477.111","article-title":"De novo discovery of mutated driver pathways in cancer","volume":"22","author":"Vandin","year":"2012","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/21\/2757\/50744699\/bioinformatics_29_21_2757.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/21\/2757\/50744699\/bioinformatics_29_21_2757.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T07:06:49Z","timestamp":1688108809000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/21\/2757\/195824"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,8,27]]},"references-count":19,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2013,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt471","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.718089120.793483017","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2013,11]]},"published":{"date-parts":[[2013,8,27]]}}}