Computational 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 infectionExploring the Role of Extracellular Vesicles in the Pathogenesis of Tuberculosis
Arya R, Shakya H, Chaurasia R, Haque A, Kim J. Exploring the Role of Extracellular Vesicles in the Pathogenesis of Tuberculosis. Genes 2024, 15: 434. PMID: 38674369, PMCID: PMC11049626, DOI: 10.3390/genes15040434.Peer-Reviewed Original ResearchConceptsProtein-protein interaction networkRNA-seq datasetsExtracellular vesiclesTB patientsHealthy controlsResponse regulatorCellular processesInteraction networkPathogenesis of tuberculosisExosome biogenesisImmune response regulationImmune cell profilesDEGsPotential biomarkersVAMP5Immune cell infiltration analysisGenesTherapeutic targetImmune cellsGlobal health concernDiagnostic performanceVesiclesDisease progressionTreatment outcomesAccurate diagnosis