An integrative ENCODE resource for cancer genomics
Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. An integrative ENCODE resource for cancer genomics. Nature Communications 2020, 11: 3696. PMID: 32728046, PMCID: PMC7391744, DOI: 10.1038/s41467-020-14743-w.Peer-Reviewed Original ResearchConceptsCell typesFunctional genomics datasetsEffect of MycStem-like stateNetwork-based annotationUncharacterized RBPsOncogenic TFSTARR-seqOncogene knockdownTranscription factorsGenomic datasetsOncogenic transformationGenome interpretationUniversal annotationCancer genomicsDifferential expressionSiRNA knockdownLuciferase assayTargeted validationRegulatorTumor transitionCustom annotationsAnnotationKnockdownCoherent workflowDiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring
Zhang J, Liu J, Lee D, Lou S, Chen Z, Gürsoy G, Gerstein M. DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. BMC Bioinformatics 2020, 21: 281. PMID: 32615918, PMCID: PMC7333332, DOI: 10.1186/s12859-020-03605-3.Peer-Reviewed Original ResearchConceptsCo-regulation networkCo-regulatory networkNetwork rewiringDisease regulatorsGenome-wide binding profilesGM12878 cell lineRNA polymerase IITumor suppressor BRCA1Transcription factor bindsChIP-seq dataDifferential graphical modelsBinding profileComplete binding profilesKey TFsPolymerase IIHub regulatorsPhenotypic variationFactor bindsGene expressionExpression changesCancerous stateRisk genesRegulatorCell linesCoordinated mannerTopicNet: a framework for measuring transcriptional regulatory network change
Lou S, Li T, Kong X, Zhang J, Liu J, Lee D, Gerstein M. TopicNet: a framework for measuring transcriptional regulatory network change. Bioinformatics 2020, 36: i474-i481. PMID: 32657410, PMCID: PMC7355251, DOI: 10.1093/bioinformatics/btaa403.Peer-Reviewed Original ResearchMeSH KeywordsChromatin Immunoprecipitation SequencingGene Regulatory NetworksHumansTranscription FactorsConceptsRegulatory network changesTranscription factorsCellular statesDifferent regulatory programsCollection of genesDifferent cellular statesParticular cellular stateParticular transcription factorsRegulatory network connectivityKey transcription factorGene expression dataChromatin immunoprecipitationRegulatory networksCell statesExpression dataRegulatory programsHuman cellsDifferential survivalDiverse groupSupplementary dataDynamic changesLoss of targetImmunoprecipitationGenesActivity differences