2019
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
Zhou B, Ho S, Greer S, Zhu X, Bell J, Arthur J, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney M, Haraksingh R, Song G, Ji H, Perrin D, Wong W, Abyzov A, Urban A. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. Genome Research 2019, 29: 472-484. PMID: 30737237, PMCID: PMC6396411, DOI: 10.1101/gr.234948.118.Peer-Reviewed Original ResearchConceptsWhole-genome analysisStructural variantsFunctional genomicsEpigenomic dataAllele-specific DNA methylationComprehensive whole-genome analysisWhole-genome bisulfite sequencing dataGenomic structural featuresCopy numberLinked-read sequencingAllele-specific expressionEntire chromosome armsBisulfite sequencing dataAllele-specific deletionsComplex structural variantsTumor suppressor geneEpigenomic characteristicsChromosome armsGenome sequenceChromosome segmentsDNA methylationRNA-seqGenome characteristicsRetrotransposon insertionGenomic variant information
2012
Architecture of the human regulatory network derived from ENCODE data
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O’Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature 2012, 489: 91-100. PMID: 22955619, PMCID: PMC4154057, DOI: 10.1038/nature11245.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell LineDNAEncyclopedias as TopicGATA1 Transcription FactorGene Expression ProfilingGene Regulatory NetworksGenome, HumanGenomicsHumansK562 CellsMolecular Sequence AnnotationOrgan SpecificityPhosphorylationPolymorphism, Single NucleotideProtein Interaction MapsRegulatory Sequences, Nucleic AcidRNA, UntranslatedSelection, GeneticTranscription FactorsTranscription Initiation SiteConceptsTranscription factorsRegulatory networksHuman transcriptional regulatory networkHuman regulatory networkSpecific genomic locationsTranscription-related factorsState of genesTranscriptional regulatory networksAllele-specific activityPersonal genome sequencesGenomic locationStrong selectionGenome sequenceENCODE dataGenomic informationInformation-flow bottlenecksRegulatory informationConnected network componentsCombinatorial fashionInfluences expressionHuman biologyBinding informationNetwork motifsCo-associationGenes