2008
Genomic Androgen Receptor-Occupied Regions with Different Functions, Defined by Histone Acetylation, Coregulators and Transcriptional Capacity
Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA. Genomic Androgen Receptor-Occupied Regions with Different Functions, Defined by Histone Acetylation, Coregulators and Transcriptional Capacity. PLOS ONE 2008, 3: e3645. PMID: 18997859, PMCID: PMC2577007, DOI: 10.1371/journal.pone.0003645.Peer-Reviewed Original ResearchConceptsTranscription factorsChromatin immunoprecipitation-microarray analysisTarget gene expression levelsSame transcription factorHuman genomic DNAGene expression levelsChromatin structureSuch genesKnockout experimentsHistone acetylationTarget genesEnhancer activityTranscriptional capacityDNA locationsGenomic androgen receptorsGene expressionGenomic DNAMicroarray analysisProstate cancer cellsDifferential regulationGenesLuciferase reporterDiverse mechanismsHigh-throughput elucidationContinuous stretchProgressive recruitment of Runx2 to genomic targets despite decreasing expression during osteoblast differentiation
Pregizer S, Baniwal SK, Yan X, Borok Z, Frenkel B. Progressive recruitment of Runx2 to genomic targets despite decreasing expression during osteoblast differentiation. Journal Of Cellular Biochemistry 2008, 105: 965-970. PMID: 18821584, PMCID: PMC2591066, DOI: 10.1002/jcb.21900.Peer-Reviewed Original ResearchConceptsOC promoterGenomic targetsOsteoblast differentiationNovel genomic targetsChIP-chip analysisChromatin immunoprecipitation assaysDNA-binding abilityDNA-binding activityOsteoblast transcription factorSuch stringent controlTranscriptional controlMRNA levelsTranslational controlTranscription factorsImmunoprecipitation assaysMC3T3-E1 culturesRunx2 mRNA levelsOC mRNA levelsOsteoblast phenotypeRunx2 mRNAPromoterRunx2Protein amountOC expressionStringent control
2007
Inferring activity changes of transcription factors by binding association with sorted expression profiles
Cheng C, Yan X, Sun F, Li LM. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics 2007, 8: 452. PMID: 18021409, PMCID: PMC2194743, DOI: 10.1186/1471-2105-8-452.Peer-Reviewed Original ResearchConceptsTranscription factorsExpression profilesMicroarray dataTarget gene selectionPost-transcriptional modificationsChIP-chip dataMicroarray expression profilesExpression differentiationLow expression levelsProfile of expressionTarget genesRegulatory mechanismsGene expressionBiological processesMicroarray studiesAffinity dataGene selectionSame machineryExpression levelsGenesActivity changesSignificance cutoffDifferentiationMeaningful hypothesesAffinity scores