2024
OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers
Zhang Y, Liu K, Xu Z, Li B, Wu X, Fan R, Yao X, Wu H, Duan C, Gong Y, Chen K, Zeng J, Li L, Xu H. OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers. Nucleic Acids Research 2024, gkae1098. PMID: 39558172, DOI: 10.1093/nar/gkae1098.Peer-Reviewed Original ResearchRNA-binding proteinsAlternative splicing eventsAS eventsSplicing eventsAlternative splicingPotential RNA-binding proteinsRegulate alternative splicing eventsTCGA cancersRNA-binding motifRNA-seq dataRegulate gene expressionMRNA expression dataECLIP-seqGTEx tissuesENCODE projectAbnormal alternative splicingIntron sequencesSplicing analysisRNA-seqExpression dataProtein complexesMinigene constructsSplicingGene expressionPerturbation experiments
2021
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers
Zhang Y, Yao X, Zhou H, Wu X, Tian J, Zeng J, Yan L, Duan C, Liu H, Li H, Chen K, Hu Z, Ye Z, Xu H. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Research 2021, 50: d1340-d1347. PMID: 34554251, PMCID: PMC8728274, DOI: 10.1093/nar/gkab851.Peer-Reviewed Original ResearchConceptsAlternative splicingCancer-specific splicing eventsDifferential alternative splicingHuman cancersTCGA tumor samplesSplicing differencesSplicing eventsProtein complexityAdjacent normal samplesSplicingGene expressionSplicing dataNormal samplesAbnormal splicingIntegrative viewMRNA levelsDifferential analysisTumor samplesTranscripts
2015
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action
Sun J, Zhao M, Jia P, Wang L, Wu Y, Iverson C, Zhou Y, Bowton E, Roden D, Denny J, Aldrich M, Xu H, Zhao Z. Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLOS Computational Biology 2015, 11: e1004202. PMID: 26083494, PMCID: PMC4470683, DOI: 10.1371/journal.pcbi.1004202.Peer-Reviewed Original ResearchConceptsGWAS datasetsPathway networkDisease genesGenome-wide association study datasetDrug targetsSignal transduction networksSignal transduction cascadeMultiple signaling pathwaysDrug-induced gene expressionNovel drug targetsTransduction networksTransduction cascadeEnrichment analysisGene expressionCommon genesMolecular mechanismsSignaling pathwaysGenesNovel MycLiterature miningMolecular modePathwayMetformin actionDrug actionDisease pathogenesis