2017
Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression
Fiziev P, Akdemir K, Miller J, Keung E, Samant N, Sharma S, Natale C, Terranova C, Maitituoheti M, Amin S, Martinez-Ledesma E, Dhamdhere M, Axelrad J, Shah A, Cheng C, Mahadeshwar H, Seth S, Barton M, Protopopov A, Tsai K, Davies M, Garcia B, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Reports 2017, 19: 875-889. PMID: 28445736, PMCID: PMC5473172, DOI: 10.1016/j.celrep.2017.03.078.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationCell LineCell ProliferationChromatinChromatin ImmunoprecipitationDisease-Free SurvivalEpigenomicsHistone Deacetylase InhibitorsHistone DeacetylasesHistonesHumansHydroxamic AcidsKaplan-Meier EstimateMelanomaPrincipal Component AnalysisPTEN PhosphohydrolaseRNA InterferenceRNA, Small InterferingSignal TransductionVorinostatConceptsChromatin state transitionsMelanoma progressionChromatin state changesGene expression patternsCancer regulatory genesChromatin stateEpigenomic profilingEpigenomic changesEpigenomic analysisTumorigenic stateEpigenetic modificationsTranscriptomic analysisRegulatory regionsHistone acetylationAcetylation changesHistone deacetylase inhibitorsExpression patternsHyperproliferative phenotypeAcetylation levelsTumorigenic cellsHuman melanoma cellsFunctional rolePhenotypic modelDeacetylase inhibitorsMelanoma cells
2011
The dChip survival analysis module for microarray data
Amin S, Shah P, Yan A, Adamia S, Minvielle S, Avet-Loiseau H, Munshi N, Li C. The dChip survival analysis module for microarray data. BMC Bioinformatics 2011, 12: 72. PMID: 21388547, PMCID: PMC3068974, DOI: 10.1186/1471-2105-12-72.Peer-Reviewed Original ResearchConceptsAnalysis moduleUser-friendly wayDemonstration dataMicroarray data analysisAnalysis functionsFast computationSoftware packageSoftwareSignificant chromosome regionsMicroarray dataMinimal learning curveGene expressionDChip softwareModuleGenome-wide copy number alterationsData analysisSNP array dataSurvival gene signaturesCopy number dataChromosome displayContext of genesUsersCopy number alterationsChromosome regionsClustering