2021
Multi-omics analysis to identify susceptibility genes for colorectal cancer
Yuan Y, Bao J, Chen Z, Villanueva A, Wen W, Wang F, Zhao D, Fu X, Cai Q, Long J, Shu X, Zheng D, Moreno V, Zheng W, Lin W, Guo X. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Human Molecular Genetics 2021, 30: 321-330. PMID: 33481017, PMCID: PMC8485221, DOI: 10.1093/hmg/ddab021.Peer-Reviewed Original ResearchMeSH KeywordsCarcinogenesisCell Line, TumorCell ProliferationColorectal NeoplasmsDNA MethylationGene Expression Regulation, NeoplasticGenetic Association StudiesGenetic Predisposition to DiseaseGenomeGenome-Wide Association StudyHumansNerve Tissue ProteinsPolymorphism, Single NucleotideRepressor ProteinsRisk FactorsTranscriptomeConceptsGenome-wide association studiesMulti-omics analysisSusceptibility genesTarget genesPutative target genesGWAS-identified variantsMost genetic variantsDNA methylation dataNovel susceptibility genesGenotype-Tissue ExpressionGenetic risk lociPutative susceptibility genesGene regulationIntergenic regionPathogenic dysregulationCancer Genome AtlasEpithelial-mesenchymal transitionRisk lociGene expressionMethylation dataAssociation studiesGenesCell behaviorGenetic variantsGenome Atlas
2019
Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression
Bar C, Cohen I, Zhao D, Pothula V, Litskevitch A, Koseki H, Zheng D, Ezhkova E. Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression. Cell Reports 2019, 28: 257-266.e5. PMID: 31269445, PMCID: PMC6921245, DOI: 10.1016/j.celrep.2019.06.011.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBody PatterningCell CycleChromatin ImmunoprecipitationChromatin Immunoprecipitation SequencingCyclin-Dependent Kinase Inhibitor p16Epigenesis, GeneticEpitheliumGene Expression Regulation, DevelopmentalGene OntologyHedgehog ProteinsMiceMice, KnockoutMicroscopy, Electron, ScanningPolycomb Repressive Complex 1Polycomb Repressive Complex 2RNA-SeqSignal TransductionTaste BudsTongueConceptsGene expressionPolycomb Repressive Complex 1Spatial gene expression patternsRepressive Complex 1Gene expression patternsCell gene expressionChromatin regulatorsTissue patterningSonic hedgehog expressionEpigenetic regulationNiche structureExpression patternsCell genesEpithelial progenitorsHedgehog expressionShhEctopic ShhTaste cellsPapilla structuresTissue patternsExpressionCellsPatterningProper maintenanceComplexes 1
2018
PRC1 preserves epidermal tissue integrity independently of PRC2
Cohen I, Zhao D, Menon G, Nakayama M, Koseki H, Zheng D, Ezhkova E. PRC1 preserves epidermal tissue integrity independently of PRC2. Genes & Development 2018, 33: 55-60. PMID: 30567998, PMCID: PMC6317312, DOI: 10.1101/gad.319939.118.Peer-Reviewed Original ResearchConceptsAdhesion genesEpidermal tissue integrityLoss of PRC1PRC1 functionChromatin regulatorsEpigenetic regulationMolecular dissectionPRC2PRC1Gene expressionTissue developmentSkin morphogenesisFunctional linkSkin fragility syndromeEpidermal stratificationEpidermal integrityTissue integrityGenesExpressionH3K27me3Fragility syndromeMorphogenesisRegulatorCobindingRegulationEnriched expression of genes associated with autism spectrum disorders in human inhibitory neurons
Wang P, Zhao D, Lachman HM, Zheng D. Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons. Translational Psychiatry 2018, 8: 13. PMID: 29317598, PMCID: PMC5802446, DOI: 10.1038/s41398-017-0058-6.Peer-Reviewed Original ResearchConceptsASD candidatesEnriched expressionSingle-cell transcriptomic dataSingle-cell transcriptome profilesCo-expression gene modulesDifferent developmental stagesExcitatory/inhibitory (E/I) imbalance hypothesisInhibitory neuronsGene networksTranscriptome profilesGene modulesTranscriptomic dataUpregulated genesDownstream targetsGene expressionDevelopmental stagesCell typesGenesNeuron subtypesFunctional evidenceAutism spectrum disorderExpressionASD brainCortex samplesExcitatory neurons
2017
Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis
Zhao D, Lin M, Pedrosa E, Lachman HM, Zheng D. Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis. BMC Genomics 2017, 18: 860. PMID: 29126398, PMCID: PMC5681780, DOI: 10.1186/s12864-017-4261-x.Peer-Reviewed Original ResearchConceptsMonoallelic expressionHuman brain cellsGene expressionMonoallelic gene expressionAllelic gene expressionGenome-wide levelSingle-cell RNA-seq datasetsRNA-seq data analysisAllelic expression studiesSingle-cell RNA-seq data analysisRNA-seq datasetsSingle nucleotide variantsBrain cellsCellular identityAutosomal genesNeuronal diversityExpression studiesNucleotide variantsCorrelated expressionGenesIndividual cellsHuman psychiatric disordersNeuronal cellsSingle cellsCell functionTranscriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress
Zhao D, Mokhtari R, Pedrosa E, Birnbaum R, Zheng D, Lachman HM. Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress. Molecular Autism 2017, 8: 17. PMID: 28367307, PMCID: PMC5372344, DOI: 10.1186/s13229-017-0134-z.Peer-Reviewed Original ResearchConceptsHeat shock protein familyShock protein familyWhole transcriptome analysisChromatin regulatorsAnalysis of microgliaPhenotypic phasesTranscriptome analysisProtein familyRNA-seqCellular stressMethyl-CpGRTT phenotypeRTT pathogenesisDe novo lossGene expressionM2 activation statesFemale miceDifferential expressionFunction mutationsHSP pathwayGenesMolecular pathwaysCell typesExtracellular matrixProtein 2
2012
Identification of condition‐specific reference genes from microarray data for locusts exposed to hypobaric hypoxia
Zhao DJ, Guo K, Kang L. Identification of condition‐specific reference genes from microarray data for locusts exposed to hypobaric hypoxia. FEBS Open Bio 2012, 2: 235-240. PMID: 23650605, PMCID: PMC3642161, DOI: 10.1016/j.fob.2012.08.001.Peer-Reviewed Original ResearchGene expression stabilityReference genesHousekeeping genesExpression stabilityGene expressionNovel candidate reference genesMicroarray dataQuantitative polymerase chain reactionLarge-scale gene expression dataClassical housekeeping genesCandidate reference genesReliable reference genesGene expression dataGenes 18STranscriptional responseStable genesExpression dataGenesΒ-actinReal-time quantitative polymerase chain reactionLocust muscleGeNormNormFinderExpressionPolymerase chain reaction