2024
Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts
Itai T, Yan F, Liu A, Dai Y, Iwaya C, Curtis S, Leslie E, Simon L, Jia P, Chen X, Iwata J, Zhao Z. Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts. Human Genetics And Genomics Advances 2024, 5: 100313. PMID: 38807368, PMCID: PMC11318074, DOI: 10.1016/j.xhgg.2024.100313.Peer-Reviewed Original ResearchDe novo variantsCPO geneOMIM genesGene functionScRNA-seq data analysisOrofacial cleftsMan (OMIMScRNA-seq analysisOnline Mendelian InheritanceSingle-cell RNA sequencingSingle-cell expression profilesInvestigate gene functionCleft palateScRNA-seqGene setsCellular expression profilesMendelian inheritanceGenetic variantsRNA sequencingOrofacial clefting genesContextual geneGenesExpression patternsCongenital birth defectsExpression profilesUnveiling Gene Interactions in Alzheimer’s Disease by Integrating Genetic and Epigenetic Data with a Network-Based Approach
Sanders K, Manuel A, Liu A, Leng B, Chen X, Zhao Z. Unveiling Gene Interactions in Alzheimer’s Disease by Integrating Genetic and Epigenetic Data with a Network-Based Approach. Epigenomes 2024, 8: 14. PMID: 38651367, PMCID: PMC11036294, DOI: 10.3390/epigenomes8020014.Peer-Reviewed Original ResearchEnrichment analysisGenome-wide association studiesAlzheimer's diseaseDense module searchDNA methylation dataGene network modulesFunctional enrichment analysisGWAS signalsGWAS datasetsTarget enrichmentAssociation studiesGenetic dataEpigenetic signalsNetwork-based toolCause of dementiaGene interactionsAD pathogenesisMethylation dataDNA methylationBIN1 geneAD pathologyComplex diseasesGenesSignificant cell typeDrug repurposing efforts
2011
Disease-associated DNA methylationin Inflammatory Bowel Disease subtypes Crohn's disease and Ulcerative Colitis
lin Z, Yu W, Chen X, Hegarty J, Faber P, Wang Y, Poritz L, Fan J, Koltun W. Disease-associated DNA methylationin Inflammatory Bowel Disease subtypes Crohn's disease and Ulcerative Colitis. Inflammatory Bowel Diseases 2011, 17: s78-s78. DOI: 10.1097/00054725-201112002-00257.Peer-Reviewed Original ResearchAberrant DNA methylationDNA methylationTranscriptional regulationNondiseased tissueTissue-specific DNA methylationDNA methylation eventsGene transcriptional regulationDisease-associated changesMethylation eventsCpG methylationIntron 5Protein processingDiseased tissuesColon tissuesGenetic variationGenomic DNAMethylation assayCell signalingEpigenetic alterationsCpGGenesCell adhesionFunctional studiesIntestinal biologyCellular transportGenes Differentially Regulated by NKX2-3 in B Cells Between Ulcerative Colitis and Crohn’s Disease Patients and Possible Involvement of EGR1
Yu W, Lin Z, Hegarty J, Chen X, Kelly A, Wang Y, Poritz L, Koltun W. Genes Differentially Regulated by NKX2-3 in B Cells Between Ulcerative Colitis and Crohn’s Disease Patients and Possible Involvement of EGR1. Inflammation 2011, 35: 889-899. PMID: 21968973, DOI: 10.1007/s10753-011-9390-9.Peer-Reviewed Original ResearchConceptsNKX2-3B cellsCDNA microarrayUlcerative colitisCrohn's diseaseCell growthGenesCD patientsEGR1MRNA expressionNKX2CD pathogenesisDiseased intestinal tissueKnockdownChronic intestinal inflammationDisease patientsCrohn's disease patientsIntestinal inflammationIntestinal tissueUC patientsImmune responseCDNAPatientsMicroarrayColitisNKX2-3 Transcriptional Regulation of Endothelin-1 and VEGF Signaling in Human Intestinal Microvascular Endothelial Cells
Yu W, Hegarty J, Berg A, Chen X, West G, Kelly A, Wang Y, Poritz L, Koltun W, Lin Z. NKX2-3 Transcriptional Regulation of Endothelin-1 and VEGF Signaling in Human Intestinal Microvascular Endothelial Cells. PLOS ONE 2011, 6: e20454. PMID: 21637825, PMCID: PMC3102722, DOI: 10.1371/journal.pone.0020454.Peer-Reviewed Original ResearchMeSH KeywordsAdultCell LineDemographyEndothelial CellsEndothelin-1FemaleGene Expression RegulationGene Knockdown TechniquesGene Regulatory NetworksHomeodomain ProteinsHumansInflammatory Bowel DiseasesIntestinesMaleMicrovesselsMiddle AgedNitric Oxide Synthase Type IIIOligonucleotide Array Sequence AnalysisPhosphatidylinositol 3-KinasesProto-Oncogene Proteins c-aktReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionRNA, MessengerRNA, Small InterferingSignal TransductionTranscription FactorsTranscription, GeneticVascular Endothelial Growth Factor AConceptsInflammatory bowel disease pathogenesisHuman intestinal microvascular endothelial cellsNKX2-3CDNA microarrayIntestinal microvascular endothelial cellsGene expressionValidity of microarraysPI3KExpression levelsMicrovascular endothelial cellsRegulating endothelin-1Intestinal tissueRelated signaling pathwaysGene networksCellular functionsBiological functionsPathogenesis of inflammatory bowel diseaseInflammatory bowel diseasePathway analysisGenesSignaling pathwayMetabolic processesAssociated with inflammatory bowel diseaseVEGF signalingMRNA expression
2010
Identification of disease‐associated DNA methylation in intestinal tissues from patients with inflammatory bowel disease
Lin Z, Hegarty J, Cappel J, Yu W, Chen X, Faber P, Wang Y, Kelly A, Poritz L, Peterson B, Schreiber S, Fan J, Koltun W. Identification of disease‐associated DNA methylation in intestinal tissues from patients with inflammatory bowel disease. Clinical Genetics 2010, 80: 59-67. PMID: 20950376, DOI: 10.1111/j.1399-0004.2010.01546.x.Peer-Reviewed Original ResearchConceptsDNA methylationCpG sitesDifferentially methylated CpG sitesDNA methylation profilesLevel of gene expressionIBD-associated genesInflammatory bowel disease pathogenesisIntestinal tissueMethylation stateMultiple genesMethylation profilesMethylation assayPathogenesis of diseaseGene expressionInflammatory bowel diseaseEpigenetic factorsDNAGenetic predispositionGenesDisease subtype-specificAbnormal interactionsNon-diseaseEnvironmental factorsMethylationBowel diseaseGenes Regulated by Nkx2-3 in Sporadic and Inflammatory Bowel Disease-Associated Colorectal Cancer Cell Lines
Yu W, Lin Z, Pastor D, Hegarty J, Chen X, Kelly A, Wang Y, Poritz L, Koltun W. Genes Regulated by Nkx2-3 in Sporadic and Inflammatory Bowel Disease-Associated Colorectal Cancer Cell Lines. Digestive Diseases And Sciences 2010, 55: 3171-3180. PMID: 20165982, DOI: 10.1007/s10620-010-1138-0.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorColorectal NeoplasmsDown-RegulationGene Expression Regulation, NeoplasticGene Knockdown TechniquesHomeodomain ProteinsHumansInflammatory Bowel DiseasesOligonucleotide Array Sequence AnalysisReverse Transcriptase Polymerase Chain ReactionRNA, Small InterferingSignal TransductionTranscription FactorsWnt ProteinsConceptsNKX2-3Colorectal cancer cell linesCancer cell linesCell linesPathway analysisHigh-density cDNA microarraysCell-cell signalingRNA-mediated knockdownWnt Signaling PathwayIngenuity Pathway AnalysisB cell linesCDNA microarrayFunctional categoriesMicroarray resultsGenesIBD-associated CRCSignaling pathwayDisease patientsWnt signalingAffected pathwaysDown-regulationNKX2Up-regulatedCrohn's disease patientsKnockdownGenes regulated by Nkx2-3 in siRNA-mediated knockdown B cells: Implication of endothelin-1 in inflammatory bowel disease
Yu W, Lin Z, Hegarty J, John G, Chen X, Faber P, Kelly A, Wang Y, Poritz L, Schreiber S, Koltun W. Genes regulated by Nkx2-3 in siRNA-mediated knockdown B cells: Implication of endothelin-1 in inflammatory bowel disease. Molecular Genetics And Metabolism 2010, 100: 88-95. PMID: 20188614, DOI: 10.1016/j.ymgme.2010.02.001.Peer-Reviewed Original ResearchConceptsNKX2-3CDNA microarrayIngenuity Pathway AnalysisB cell linesSmall interfering RNA (siRNA)-mediated knockdownHigh-density cDNA microarraysInflammatory bowel diseaseDown-regulationUp-regulatedExpression profile analysisExpression levelsExpression of genesInflammatory bowel disease pathogenesisCD patientsGene networksCellular functionsProgression of inflammatory bowel diseaseResponse genesInflammatory response genesBiological functionsGene expressionMicroarray resultsGenesPathway analysisCrohn's disease
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