Understanding transcriptional regulation by integrative analysis of transcription factor binding data
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research 2012, 22: 1658-1667. PMID: 22955978, PMCID: PMC3431483, DOI: 10.1101/gr.136838.111.Peer-Reviewed Original ResearchConceptsTranscription start siteTranscriptional regulationCpG contentTranscription factor binding signalsAlternative transcription start sitesDownstream transcription start siteExpression levelsHigh CpG contentLow CpG contentChromatin featuresHistone modificationsTF bindingENCODE projectSpecific TFsTranscription factorsStart siteGene expressionIntegrative analysisDifferential expressionCell linesCoordinated mannerBinding signalsExpressionRNA extractionRegulation
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