RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins
Zhang J, Liu J, Lee D, Feng JJ, Lochovsky L, Lou S, Rutenberg-Schoenberg M, Gerstein M. RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins. Genome Biology 2020, 21: 151. PMID: 32727537, PMCID: PMC7391703, DOI: 10.1186/s13059-020-01979-4.Peer-Reviewed Original ResearchConceptsTissue-specific inputsPost-transcriptional regulationDisease-specific variantsPrioritization of variantsVariant prioritization methodsTranscriptional regulationRNA structureBinding sitesRNAProteinPrioritization methodRegulationKey roleVariantsRegulomeGenomeSplicingGermlineExonsOverall impact scoreMotifConservationAnnotationDysregulationAn 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 workflow