2024
W74. MULTI-OMICS ANALYSIS OF INTERMEDIATE PHENOTYPES REVEALS NEW RISK GENES AND PATHWAYS IN PSYCHOTIC DISORDERS
Xia C, Alliey-Rodriguez N, Tamminga C, Keshavan M, Pearlson G, Keedy S, Parker D, Bishop J, Chen C, Liu C, Gershon E. W74. MULTI-OMICS ANALYSIS OF INTERMEDIATE PHENOTYPES REVEALS NEW RISK GENES AND PATHWAYS IN PSYCHOTIC DISORDERS. European Neuropsychopharmacology 2024, 87: 141-142. DOI: 10.1016/j.euroneuro.2024.08.283.Peer-Reviewed Original ResearchTranscriptome-wide association studyGenome-wide complex trait analysisPotential causal genesQuantitative trait lociRisk genesEvent-related potentialsPolygenic risk scoresIntermediate phenotypesGene OntologyCase-control statusPsychotic disordersComplex trait analysisGenotype principal componentsIdentified risk genesGenetic correlationsMulti-omics analysisMendelian randomizationPRS-CSxPsychosis risk genesCausal genesAssociation studiesGenomic characteristicsDetect significant associationsGene associationsBipolar-Schizophrenia NetworkF85. GENETIC OVERLAP OF BRAIN STRUCTURE AND CONNECTIVITY WITH SCHIZOPHRENIA: DIFFERENT STATISTICAL METHODS PROVIDE COMPLEMENTARY INSIGHTS
Wu X, Parekh P, Lin B, Pries L, Guloksuz S, Rutten B, Andreassen O, Linden D, van der Meer D. F85. GENETIC OVERLAP OF BRAIN STRUCTURE AND CONNECTIVITY WITH SCHIZOPHRENIA: DIFFERENT STATISTICAL METHODS PROVIDE COMPLEMENTARY INSIGHTS. European Neuropsychopharmacology 2024, 87: 251. DOI: 10.1016/j.euroneuro.2024.08.496.Peer-Reviewed Original ResearchConcordant effect directionsLinkage disequilibrium score regressionGenome-wide association study dataCell adhesion molecule bindingGenetic architectureBrain measuresPolygenic scoresBrain phenotypesUnique genesGene OntologyBrain structuresConjunctional false discovery rateLinkage disequilibrium score regression analysisGenetic correlationsGenetic risk of schizophreniaComplex genetic architectureHeritable brain disorderKyoto Encyclopedia of GenesAssociated with schizophreniaInsignificant genetic correlationResting-state fMRIWhite matter integrityEncyclopedia of GenesPostsynaptic densityRisk of schizophreniaComputational reassessment of RNA-seq data reveals key genes in active tuberculosis
Arya R, Shakya H, Chaurasia R, Kumar S, Vinetz J, Kim J. Computational reassessment of RNA-seq data reveals key genes in active tuberculosis. PLOS ONE 2024, 19: e0305582. PMID: 38935691, PMCID: PMC11210783, DOI: 10.1371/journal.pone.0305582.Peer-Reviewed Original ResearchConceptsMolecular Complex DetectionProtein-protein interactionsDeregulated genesGene OntologyRNA-seq dataGene Expression Omnibus (GEO) databaseIncreasing prevalence of multidrug-resistantGEO2R online toolPrevalence of multidrug resistancePathway enrichment analysisExpression levelsPatterns of variationGene expression levelsArea under curveInnate immune responseGene networksCore genesMicroarray datasetsSTRING databaseTranscript levelsEnrichment analysisGenesInterferon SignalingInterferon-gamma signalingResponse to Mtb infectionDisturbed flow in the juxta-anastomotic area of an arteriovenous fistula correlates with endothelial loss, acute thrombus formation, and neointimal hyperplasia
Bai H, Varsanik M, Thaxton C, Ohashi Y, Gonzalez L, Zhang W, Aoyagi Y, Kano M, Yatsula B, Li Z, Pocivavsek L, Dardik A. Disturbed flow in the juxta-anastomotic area of an arteriovenous fistula correlates with endothelial loss, acute thrombus formation, and neointimal hyperplasia. AJP Heart And Circulatory Physiology 2024, 326: h1446-h1461. PMID: 38578237, PMCID: PMC11380968, DOI: 10.1152/ajpheart.00054.2024.Peer-Reviewed Original ResearchConceptsEndothelial cell lossOutflow veinChronic kidney diseaseJuxta-anastomotic areaMouse AVF modelNeointimal hyperplasiaThrombus formationAcute thrombus formationCell lossHuman AVF maturationGene OntologyAVF maturationAVF patencyEarly thrombus formationArteriovenous fistulaC57BL/6 miceClinical failureWistar ratsEndothelial lossKidney diseaseImmune responseEndothelial cellsHyperplasiaMiceAVFGenetic contribution to microglial activation in schizophrenia
Koskuvi M, Pörsti E, Hewitt T, Räsänen N, Wu Y, Trontti K, McQuade A, Kalyanaraman S, Ojansuu I, Vaurio O, Cannon T, Lönnqvist J, Therman S, Suvisaari J, Kaprio J, Blurton-Jones M, Hovatta I, Lähteenvuo M, Rolova T, Lehtonen Š, Tiihonen J, Koistinaho J. Genetic contribution to microglial activation in schizophrenia. Molecular Psychiatry 2024, 29: 2622-2633. PMID: 38519640, PMCID: PMC11420079, DOI: 10.1038/s41380-024-02529-1.Peer-Reviewed Original ResearchIngenuity Pathway AnalysisGene OntologyMajor histocompatibility complexAffected twinHuman induced pluripotent stem cell-derived microgliaExtracellular matrix signalingUpregulation of major histocompatibility complexHealthy individualsIncreased expression of inflammatory genesIncreased expressionMicroglial activationResponse to clozapineStem cell-derived microgliaBrain-resident immune cellsResponse to interleukin-1 betaPathophysiology of schizophreniaInvolvement of neuroinflammatory processesResident immune cellsExpression of inflammatory genesIncreased microglial activationInterleukin-1 betaAberrant activation of microgliaHuman cell modelsRNA sequencingInvading pathogensMulti-Omics Analysis of Gut Microbiota and Host Transcriptomics Reveal Dysregulated Immune Response and Metabolism in Young Adults with Irritable Bowel Syndrome
Chen J, Zhao T, Li H, Xu W, Maas K, Singh V, Chen M, Dorsey S, Starkweather A, Cong X. Multi-Omics Analysis of Gut Microbiota and Host Transcriptomics Reveal Dysregulated Immune Response and Metabolism in Young Adults with Irritable Bowel Syndrome. International Journal Of Molecular Sciences 2024, 25: 3514. PMID: 38542485, PMCID: PMC10970623, DOI: 10.3390/ijms25063514.Peer-Reviewed Original ResearchConceptsGut microbiotaIrritable bowel syndrome subjectsHost transcriptomeIrritable bowel syndromeMetabolic pathways of gut microbiotaTranscriptome profilingAnalysis of gut microbiotaDysbiosis of gut microbiotaDysregulated immune responseRNA-seq dataHealthy controlsMulti-omics analysisImmune responseImmune system processRNA-seqGene OntologyBowel syndromeIBS participantsMulti-OmicsMicrobiotaMetabolic pathwaysPathways of antigen processingPeripheral blood samplesGutStool samples
2023
Isoform Function Prediction Based on Heterogeneous Graph Attention Networks
Guo K, Li Y, Chen H, Shen H, Yang Y. Isoform Function Prediction Based on Heterogeneous Graph Attention Networks. 2023, 00: 522-527. DOI: 10.1109/bibm58861.2023.10386048.Peer-Reviewed Original ResearchIsoform function predictionFunction predictionIsoform functionGene OntologyMechanisms of gene regulationFunctions of isoformsProtein language modelsFunctional labelsProtein sequencesGO annotationsGene regulationSequence featuresGO termsMRNA moleculesIsoform levelsGene levelBiological processesGenesIsoformsSpecies datasetInteraction dataIntricate mechanismsProteinHeterogeneous graph attention networkAnnotationPrimary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene
Fernandez T, Williams Z, Kline T, Rajendran S, Augustine F, Wright N, Sullivan C, Olfson E, Abdallah S, Liu W, Hoffman E, Gupta A, Singer H. Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene. PLOS ONE 2023, 18: e0291978. PMID: 37788244, PMCID: PMC10547198, DOI: 10.1371/journal.pone.0291978.Peer-Reviewed Original ResearchConceptsRisk genesDe novo damaging variantsGene expression patternsWhole-exome DNA sequencingMid-fetal developmentAdditional risk genesHigh-confidence risk genesParent-child triosGene OntologyCell signalingExpression patternsCalcium ion transportFunctional convergenceCell cycleDamaging variantsGenesDNA sequencingDe novoASD probandsGenetic etiologyBiological mechanismsSequencingDNANetwork analysisIon transportIntegrated analysis of competitive endogenous RNA networks in elder patients with non-small cell lung cancer
Chen Z, Yu F, Zhu B, Li Q, Yu Y, Zong F, Liu W, Zhang M, Wu S. Integrated analysis of competitive endogenous RNA networks in elder patients with non-small cell lung cancer. Medicine 2023, 102: e33192. PMID: 36897674, PMCID: PMC9997791, DOI: 10.1097/md.0000000000033192.Peer-Reviewed Original ResearchConceptsMRNA ceRNA networkEndogenous RNA (ceRNA) networkCeRNA networkMessenger RNAsRNA networkLncRNA-miRNACompetitive endogenous RNA (ceRNA) networkLong non-coding RNAsPotential ceRNA networksNon-coding RNAsFunctions of DEmRNAsCancer-related processesCancer Genome AtlasGenome analysisGene OntologyKyoto EncyclopediaDevelopment of NSCLCGene Expression Omnibus (GEO) cohortNovel insightsGenome AtlasSurvival packageExpression levelsIntegrated analysisDEmRNAsMiRNAsBiomarker analysis from a phase I/I1b study of regorafenib and nivolumab (rego/nivo) in microsatellite stable (MSS) colorectal cancer (CRC).
Yu J, Kim Y, Mehta R, Miao R, Strosberg J, Imanirad I, Kim D, Kim R. Biomarker analysis from a phase I/I1b study of regorafenib and nivolumab (rego/nivo) in microsatellite stable (MSS) colorectal cancer (CRC). Journal Of Clinical Oncology 2023, 41: 188-188. DOI: 10.1200/jco.2023.41.4_suppl.188.Peer-Reviewed Original ResearchPathway enrichment analysisReceptor Signaling PathwayEnrichment analysisProgressive diseaseB cell activationGene OntologyCell-substrate junction assemblySignaling pathwayGO pathway enrichment analysisPositive regulation of B cell activationDownregulated pathwaysKyoto Encyclopedia of GenesSerine-type endopeptidase activityPredictive biomarkersMSS-CRCKEGG pathway enrichment analysisRegulation of B cell activationECM-receptor interactionTumor samplesEncyclopedia of GenesColorectal cancerGenomes (KEGGExtracellular matrixPre-treatment tumor samplesGene Set Enrichment AnalysisCpH methylome analysis in human cortical neurons identifies novel gene pathways and drug targets for opioid use disorder
Nagamatsu S, Rompala G, Hurd Y, Núñez-Rios D, Montalvo-Ortiz J, Group T, Alvarez V, Benedek D, Che A, Cruz D, Davis D, Girgenti M, Hoffman E, Holtzheimer P, Huber B, Kaye A, Krystal J, Labadorf A, Keane T, Logue M, McKee A, Marx B, Mash D, Miller M, Noller C, JM-O, Scott W, Schnurr P, Stein T, Ursano R, Williamson D, Wolf E, Young K. CpH methylome analysis in human cortical neurons identifies novel gene pathways and drug targets for opioid use disorder. Frontiers In Psychiatry 2023, 13: 1078894. PMID: 36745154, PMCID: PMC9892724, DOI: 10.3389/fpsyt.2022.1078894.Peer-Reviewed Original ResearchOpioid use disorderOrbital frontal cortexDNA methylationKEGG enrichment analysisUse disordersMCPH lociTreatment of OUDGene OntologyEnrichment analysisOpioid-related drugsCpG sitesDrug targetsOxidative bisulfite sequencingImportant biological pathwaysDrug interaction analysisDrug-gene interaction databaseNervous system developmentSmoking statusBrain BankCortical neuronsFrontal cortexNeuronal nucleiHuman studiesGene regulationMethylome analysis
2021
Impaired GSH biosynthesis disrupts eye development, lens morphogenesis and PAX6 function
Thompson B, Chen Y, Davidson EA, Garcia-Milian R, Golla JP, Apostolopoulos N, Orlicky DJ, Schey K, Thompson DC, Vasiliou V. Impaired GSH biosynthesis disrupts eye development, lens morphogenesis and PAX6 function. The Ocular Surface 2021, 22: 190-203. PMID: 34425299, PMCID: PMC8560581, DOI: 10.1016/j.jtos.2021.08.010.Peer-Reviewed Original ResearchConceptsHEK293T cellsEye developmentGSH biosynthesisTransactivation activityPax6 functionReactive oxygen speciesSubsequent gene ontologyCell identity genesButhionine sulfoximineEpithelial cell identityRNA-seq analysisIngenuity Pathway AnalysisKey upstream regulatorIdentity genesCell identityGene OntologyRNA-seqImmune response genesBioinformatics analysisResponse genesGlutathione biosynthesisLens morphogenesisMolecular consequencesUpstream regulatorMicrophthalmia phenotypeThe Effect of Interleukin-4 and Dexamethasone on RNA-Seq-Based Transcriptomic Profiling of Human Podocytes: A Potential Role in Minimal Change Nephrotic Syndrome
Lee J, Ko Y, Lee C, Jeon N, Lee K, Oh J, Kronbichler A, Saleem M, Lim B, Shin J. The Effect of Interleukin-4 and Dexamethasone on RNA-Seq-Based Transcriptomic Profiling of Human Podocytes: A Potential Role in Minimal Change Nephrotic Syndrome. Journal Of Clinical Medicine 2021, 10: 496. PMID: 33535372, PMCID: PMC7866993, DOI: 10.3390/jcm10030496.Peer-Reviewed Original ResearchGene OntologyHuman podocytesRNA-seq-based transcriptome profilingIL-4-induced changesWhole-transcriptome sequencingRelevant biological pathwaysCytoskeleton organizationGO analysisInterleukin-4 treatmentCell signalingTranscriptome profilingPodocyte genesBiological pathwaysGenesTranscriptomeInterleukin-4Pathogenic effectsExpression levelsNephrotic syndromeDEGsEffect of interleukin-4PathwayPodocytesMinimal change nephrotic syndromePathogenesis of nephrotic syndrome
2020
Genetically-regulated transcriptomics & copy number variation of proctitis points to altered mitochondrial and DNA repair mechanisms in individuals of European ancestry
Pathak GA, Polimanti R, Silzer TK, Wendt FR, Chakraborty R, Phillips NR. Genetically-regulated transcriptomics & copy number variation of proctitis points to altered mitochondrial and DNA repair mechanisms in individuals of European ancestry. BMC Cancer 2020, 20: 954. PMID: 33008348, PMCID: PMC7530964, DOI: 10.1186/s12885-020-07457-1.Peer-Reviewed Original ResearchConceptsWhole blood tissuesCopy number variationsNumber variationsGene expressionGenome-Wide Human SNP Array 6.0Mitochondrial apoptosis regulationRNA-seq informationGenetic variantsDNA repair mechanismsGene expression changesDNA repair processesGene expression associationsGene expression profilesGene network informationDNA repair genesCopy number dataCopy number analysisGene OntologyApoptosis regulationDNA repairEnriched pathwaysEnriched processesOrganismal injuryTranscriptomic profilesExpression changesQuantitative proteomics revealed the putative biomarker for detection of early-stage intra-mammary gland infection in cow
Bathla S, Sindhu A, Kumar S, Dubey S, Pattnaik S, Rawat P, Chopra A, Mohanty A. Quantitative proteomics revealed the putative biomarker for detection of early-stage intra-mammary gland infection in cow. Journal Of Proteins And Proteomics 2020, 11: 173-181. DOI: 10.1007/s42485-020-00045-8.Peer-Reviewed Original ResearchSomatic cell countCalifornia Mastitis TestMammary gland infectionGland infectionKaran FriesMastitis TestClinical mastitisMilk constituentsMilk productionCollected milkDairy industryAnimal healthBovine milkMastitisMilkQuantitative proteomicsDown-regulated proteinsMammary glandSub-clinicalProtein-protein interactionsMS-based quantitative proteomicsESI-Q-TOFPotential protein targetsIsobaric tagsGene OntologyDifferential regulation of the immune system in a brain-liver-fats organ network during short-term fasting
Huang S, Makhlouf M, AbouMoussa E, Segura M, Mathew L, Wang K, Leung M, Chaussabel D, Logan D, Scialdone A, Garand M, Saraiva L. Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting. Molecular Metabolism 2020, 40: 101038. PMID: 32526449, PMCID: PMC7339127, DOI: 10.1016/j.molmet.2020.101038.Peer-Reviewed Original ResearchConceptsShort-term fastingGene Ontology enrichment analysisOntology enrichment analysisReactome pathway analysisInnate immune signalingCombination of multivariate analysisImmune systemPriming of adaptive immunityChronic immunological disordersTranscriptional dynamicsGene setsGene OntologyWhite adipose tissueAdipose tissueProtein dataRNA sequencingBrown adipose tissueExpression analysisEnrichment analysisImmune signalingProfiles of miceDifferential regulationBiological pathwaysPathway analysisMolecular mechanismsAbnormal Peripheral Neutrophil Transcriptome in Newly Diagnosed Type 2 Diabetes Patients
Lin Q, Zhou W, Wang Y, Huang J, Hui X, Zhou Z, Xiao Y. Abnormal Peripheral Neutrophil Transcriptome in Newly Diagnosed Type 2 Diabetes Patients. Journal Of Diabetes Research 2020, 2020: 9519072. PMID: 32377527, PMCID: PMC7195634, DOI: 10.1155/2020/9519072.Peer-Reviewed Original ResearchConceptsType 2 diabetes patientsGene OntologyType 2 diabetesComprehensive transcriptome analysisKEGG pathway enrichment analysisCytokine receptor interaction pathwayMyeloid leukocyte activationPathway enrichment analysisReceptor interaction pathwayQPCR of genesGene expression analysisDiabetes patientsHealthy controlsUpregulated DEGsTranscriptome analysisTranscriptome levelGO analysisKEGG pathwaysRNA sequencingCell adhesion moleculeExpression analysisEnrichment analysisInteraction pathwayMolecular mechanismsDEGs
2019
Human chromatin remodeler cofactor, RNA interactor, eraser and writer sperm RNAs responding to obesity
Swanson GM, Estill M, Diamond MP, Legro RS, Coutifaris C, Barnhart KT, Huang H, Hansen KR, Trussell JC, Coward RM, Zhang H, Goodrich R, Krawetz SA. Human chromatin remodeler cofactor, RNA interactor, eraser and writer sperm RNAs responding to obesity. Epigenetics 2019, 15: 32-46. PMID: 31354029, PMCID: PMC6961666, DOI: 10.1080/15592294.2019.1644880.Peer-Reviewed Original ResearchConceptsSperm RNASperm DNA methylationChromosome organizationCoregulatory networkGene OntologyDNA methylationResponse pathwaysCellular stressRNA elementsRNAInteractorsErasersCofactorOvarian stimulation (AMIGOS) trialMethylationObesity-related inflammationTranscriptsMeasures of obesityAdipogenesisPathwayMultiple gestationsStimulation trialsAnimal modelsBMIHuman studiesHistone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility
Robson A, Makova SZ, Barish S, Zaidi S, Mehta S, Drozd J, Jin SC, Gelb BD, Seidman CE, Chung WK, Lifton RP, Khokha MK, Brueckner M. Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 14049-14054. PMID: 31235600, PMCID: PMC6628794, DOI: 10.1073/pnas.1808341116.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell MovementCell ProliferationChromatin Assembly and DisassemblyCiliaDisease Models, AnimalEpigenesis, GeneticGene Expression Regulation, NeoplasticHeartHeart Defects, CongenitalHistonesHumansLoss of Function MutationMiceRegulatory Factor X Transcription FactorsSignal TransductionUbiquitin-Conjugating EnzymesUbiquitin-Protein LigasesUbiquitinationXenopusConceptsHistone H2B monoubiquitinationCilia genesH2B monoubiquitinationCilia motilityFunctional gene ontologyHuman congenital heart diseaseUpstream transcriptional regulatorsTissue-specific expressionChromatin remodeling genesChromatin remodelingEpigenetic controlH2Bub1 levelsTranscriptional regulatorsChIP-seqDepletion phenotypeGene OntologyGenomic analysisTranscription factorsKnockdown resultsLeft-right asymmetryCilia functionHeart developmentH2Bub1RNF20Complex consistingIdentification of gene ontology and pathways implicated in suicide behavior: Systematic review and enrichment analysis of GWAS studies
González‐Castro T, Tovilla‐Zárate C, Genis‐Mendoza A, Juárez‐Rojop I, Nicolini H, López‐Narváez M, Martínez‐Magaña J. Identification of gene ontology and pathways implicated in suicide behavior: Systematic review and enrichment analysis of GWAS studies. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2019, 180: 320-329. PMID: 31045331, DOI: 10.1002/ajmg.b.32731.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesBiological process gene ontologyGene OntologyProtein localizationPositive regulationKEGG pathwaysEnrichment analysisGenomes (KEGG) biological pathwaysHeterotypic cell-cell adhesionCell-cell adhesionGlucose importKyoto EncyclopediaGO analysisCardiomyopathy pathwaysGWAS studiesBiological pathwaysAssociation studiesGenesGenetic contributorsMultiple large-scale studiesEndopeptidase activityInsulin stimulusPathwayRegulationMuscle cell contraction
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