2022
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective
Gu J, Dai J, Lu H, Zhao H. Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective. Genomics Proteomics & Bioinformatics 2022, 21: 164-176. PMID: 35569803, PMCID: PMC10373092, DOI: 10.1016/j.gpb.2021.08.017.Peer-Reviewed Original ResearchConceptsGlobal expression patternsHuman transcriptomeExpression patternsHuman genesTemporal gene expression patternsVaried expression patternsGene expression patternsInternal reference genesHuman genomeTranscriptomeRegulatory codeGene clusteringMolecular mechanismsReference genesStable expressionIslet beta cellsHuman diseasesGenesExpression measurementsBeta cellsUbiquitouslyPhysiological conditionsValuable resourceComprehensive characterizationExtensive collection
2019
A statistical framework for cross-tissue transcriptome-wide association analysis
Hu Y, Li M, Lu Q, Weng H, Wang J, Zekavat SM, Yu Z, Li B, Gu J, Muchnik S, Shi Y, Kunkle BW, Mukherjee S, Natarajan P, Naj A, Kuzma A, Zhao Y, Crane PK, Lu H, Zhao H. A statistical framework for cross-tissue transcriptome-wide association analysis. Nature Genetics 2019, 51: 568-576. PMID: 30804563, PMCID: PMC6788740, DOI: 10.1038/s41588-019-0345-7.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association analysisAssociation analysisGene-trait associationsGene expression dataGene expression levelsGenetic architectureComplex traitsMore genesGene expressionSingle tissueExpression dataAssociation resultsExpression levelsPowerful approachImputation modelHuman tissuesImputation accuracyGenotypesStatistical frameworkTissueGenesKey componentTraitsPowerful metricExpression
2017
RNA‐seq Based Transcription Characterization of Fusion Breakpoints as a Potential Estimator for Its Oncogenic Potential
Gu J, Chukhman M, Lu Y, Liu C, Liu S, Lu H. RNA‐seq Based Transcription Characterization of Fusion Breakpoints as a Potential Estimator for Its Oncogenic Potential. BioMed Research International 2017, 2017: 9829175. PMID: 29181411, PMCID: PMC5664375, DOI: 10.1155/2017/9829175.Peer-Reviewed Original ResearchConceptsOncogenic potentialFusion mutationsFusion geneHigh-throughput sequencing technologyClonal evolution theoryTranscriptome sequencing datasetsLarger clonal sizeSequencing technologiesSequencing datasetsGene fusionsClone ratioGenesFusion breakpointsGenomic alterationsMutationsFunctional featuresNeoplastic cellsTMPRSS2-ERGNormal samplesClonal sizeTumor samplesRecent studiesCellsEvolution theoryBreakpoints
2015
Identification of cancer‐related genes and motifs in the human gene regulatory network
Carson M, Gu J, Yu G, Lu H. Identification of cancer‐related genes and motifs in the human gene regulatory network. IET Systems Biology 2015, 9: 128-134. PMID: 26243828, PMCID: PMC8687282, DOI: 10.1049/iet-syb.2014.0058.Peer-Reviewed Original Research
2013
Deep mRNA Sequencing Analysis to Capture the Transcriptome Landscape of Zebrafish Embryos and Larvae
Yang H, Zhou Y, Gu J, Xie S, Xu Y, Zhu G, Wang L, Huang J, Ma H, Yao J. Deep mRNA Sequencing Analysis to Capture the Transcriptome Landscape of Zebrafish Embryos and Larvae. PLOS ONE 2013, 8: e64058. PMID: 23700457, PMCID: PMC3659048, DOI: 10.1371/journal.pone.0064058.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBlastulaCleavage Stage, OvumEmbryonic DevelopmentGastrulaGene Expression ProfilingGene Expression Regulation, DevelopmentalHigh-Throughput Nucleotide SequencingLarvaOligonucleotide Array Sequence AnalysisSequence Analysis, RNATranscription FactorsTranscriptomeWnt Signaling PathwayZebrafishZebrafish ProteinsConceptsTranscriptome dynamicsZebrafish embryonic developmentTranscription factor familyDistinct expression patternsRNA-seq dataGene expression profilesZygotic genomeZebrafish developmentDeep mRNATranscriptome landscapeAverage expression levelEarly gastrulationGene clusterZebrafish embryosEmbryonic developmentTranscriptomic researchFactor familyExpression patternsExpression profilesFunctional pathwaysMolecular eventsEmbryonic stagesGenesCellular mechanismsExpression levels
2011
Hox genes from the parasitic flatworm Schistosoma japonicum
Gu J, Chen S, Dou T, Xu M, Xu J, Zhang L, Hu W, Wang S, Zhou Y. Hox genes from the parasitic flatworm Schistosoma japonicum. Genomics 2011, 99: 59-65. PMID: 22100282, DOI: 10.1016/j.ygeno.2011.10.008.Peer-Reviewed Original ResearchConceptsHox gene familyHox genesGene familyFirst genome-wide characterizationGenome-wide characterizationEvolutionary developmental biologyComparative genomic analysisReal-time polymerase chain reaction experimentsGene copy numberPolymerase chain reaction experimentsOrthology groupsAxis patterningGenome assemblyDevelopmental biologyRelated speciesPhylogenetic analysisGenomic analysisGene expressionSchistosomulum stagePeptide domainGenesCopy numberAnimal speciesHigh expressionSchistosoma japonicum
2010
Analysis of floral transcription factors from Lycoris longituba
He Q, Cui S, Gu J, Zhang H, Wang M, Zhou Y, Zhang L, Huang M. Analysis of floral transcription factors from Lycoris longituba. Genomics 2010, 96: 119-127. PMID: 20406677, DOI: 10.1016/j.ygeno.2010.04.002.Peer-Reviewed Original ResearchConceptsTranscription factorsLycoris longitubaPutative transcription factorSpecific promoter regionsTF familiesTF genesL. longitubaFloral tissuesFlower formPhylogenetic analysisFloral developmentFlower colorGene transcriptionFlowering processTarget genesExpression patternsPromoter regionFlowering phaseReal-time RT-PCRGenesRT-PCRMYBMADSImportant roleTranscriptionEvolution of peroxisome proliferator-activated receptor gamma alternative splicing.
Dou T, Xu J, Gao Y, Gu J, Ji C, Xie Y, Zhou Y. Evolution of peroxisome proliferator-activated receptor gamma alternative splicing. Frontiers In Bioscience-Elite 2010, 2: 1334-43. PMID: 20515805, DOI: 10.2741/e193.Peer-Reviewed Original ResearchConceptsKa/KsGamma geneHigher Ka/KsAlternative splicing exonsDifferent transcript variantsPPAR-gamma geneAdaptive evolutionVertebrate speciesAlternative splicingEvolutionary changeAlternative exonsEST dataGenomic sequencesNew exonsPeroxisome proliferator-activated receptor gammaTranscript variantsProliferator-activated receptor gammaConstitutive counterpartExonsGenesReceptor gammaGlucose homeostasisVertebratesImportant roleSplicing