{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T04:32:29Z","timestamp":1722745949981},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: It is commonplace to predict targets of transcription factors (TFs) by sequence matching with their binding motifs. However, this ignores the particular condition of the cells. Gene expression data can provide condition-specific information, as is, e.g. exploited in Motif Enrichment Analysis.<\/jats:p>\n               <jats:p>Results: Here, we introduce a novel tool named condition-specific target prediction (CSTP) to predict condition-specific targets for TFs from expression data measured by either microarray or RNA-seq. Based on the philosophy of guilt by association, CSTP infers the regulators of each studied gene by recovering the regulators of its co-expressed genes. In contrast to the currently used methods, CSTP does not insist on binding sites of TFs in the promoter of the target genes. CSTP was applied to three independent biological processes for evaluation purposes. By analyzing the predictions for the same TF in three biological processes, we confirm that predictions with CSTP are condition-specific. Predictions were further compared with true TF binding sites as determined by ChIP-seq\/chip. We find that CSTP predictions overlap with true binding sites to a degree comparable with motif-based predictions, although the two target sets do not coincide.<\/jats:p>\n               <jats:p>Availability and implementation: CSTP is available via a web-based interface at http:\/\/cstp.molgen.mpg.de.<\/jats:p>\n               <jats:p>Contact: \u00a0meng@molgen.mpg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu066","type":"journal-article","created":{"date-parts":[[2014,2,15]],"date-time":"2014-02-15T02:04:22Z","timestamp":1392429862000},"page":"1643-1650","source":"Crossref","is-referenced-by-count":11,"title":["Condition-specific target prediction from motifs and expression"],"prefix":"10.1093","volume":"30","author":[{"given":"Guofeng","family":"Meng","sequence":"first","affiliation":[{"name":"Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany"}]},{"given":"Martin","family":"Vingron","sequence":"additional","affiliation":[{"name":"Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,2,14]]},"reference":[{"key":"2023012710533538400_btu066-B32","doi-asserted-by":"crossref","first-page":"e66278","DOI":"10.1371\/journal.pone.0066278","article-title":"Differentially expressed androgen-regulated genes in androgen-sensitive tissues reveal potential biomarkers of early prostate cancer","volume":"8","author":"Altintas","year":"2013","journal-title":"PLoS One"},{"key":"2023012710533538400_btu066-B1","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1126\/science.1162327","article-title":"Diversity and complexity in DNA recognition by transcription factors","volume":"324","author":"Badis","year":"2009","journal-title":"Science"},{"key":"2023012710533538400_btu066-B2","doi-asserted-by":"crossref","first-page":"4237","DOI":"10.4161\/cc.10.24.18383","article-title":"Distinct p53 genomic binding patterns in normal and cancer-derived human cells","volume":"10","author":"Botcheva","year":"2011","journal-title":"Cell Cycle"},{"key":"2023012710533538400_btu066-B3","doi-asserted-by":"crossref","first-page":"D102","DOI":"10.1093\/nar\/gkm955","article-title":"Jaspar, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update","volume":"36","author":"Bryne","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012710533538400_btu066-B33","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/sj.embor.7400849","article-title":"Novel c-myc target genes mediate differential effects on cell proliferation and migration","volume":"8","author":"Cappellen","year":"2007","journal-title":"EMBO Rep."},{"key":"2023012710533538400_btu066-B4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"2023012710533538400_btu066-B5","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1016\/S0168-9525(03)00140-9","article-title":"Human housekeeping genes are compact","volume":"19","author":"Eisenberg","year":"2003","journal-title":"Trends Genet."},{"key":"2023012710533538400_btu066-B6","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature11245","article-title":"Architecture of the human regulatory network derived from encode data","volume":"489","author":"Gerstein","year":"2012","journal-title":"Nature"},{"key":"2023012710533538400_btu066-B34","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ccr.2011.06.004","article-title":"A pin1\/mutant p53 axis promotes aggressiveness in breast cancer","volume":"20","author":"Girardini","year":"2011","journal-title":"Cancer Cell"},{"key":"2023012710533538400_btu066-B35","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1210\/me.2010-0409","article-title":"Hormone depletion-insensitivity of prostate cancer cells is supported by the ar without binding to classical response elements","volume":"25","author":"Gonit","year":"2011","journal-title":"Mol. 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