2024
42. STRESS EXPOSURE DYNAMICALLY REGULATES EQTL ACTIVITY IN THE POST-MORTEM BRAIN AND IN HIPSC-DERIVED NEURONS
Seah C, Signer R, Young H, Hicks E, Rusielewicz T, Bader H, Xu C, Breen M, Paull D, Yehuda R, Girgenti M, Brennand K, Huckins L. 42. STRESS EXPOSURE DYNAMICALLY REGULATES EQTL ACTIVITY IN THE POST-MORTEM BRAIN AND IN HIPSC-DERIVED NEURONS. European Neuropsychopharmacology 2024, 87: 71-72. DOI: 10.1016/j.euroneuro.2024.08.156.Peer-Reviewed Original ResearchPost-mortem brainsTranscription Factor Binding SitesAbsence of cellular stressCombat-exposed veteransFactor binding sitesImpact gene expressionBinding sitesGR binding sitesPositive regulatory activityMotif enrichmentSequence readsCRISPRi screenOpen chromatinFunctional annotationBrain regionsTraumatic stressCRISPR screensEQTLTraumatic experiencesLeading locusPTSDPerturbed genesRegulatory architectureTranscriptomic activityTranscriptomic response
2022
GATA3 Truncation Mutants Alter EMT Related Gene Expression via Partial Motif Recognition in Luminal Breast Cancer Cells
Saotome M, Poduval D, Nair R, Cooper M, Takaku M. GATA3 Truncation Mutants Alter EMT Related Gene Expression via Partial Motif Recognition in Luminal Breast Cancer Cells. Frontiers In Genetics 2022, 13: 820532. PMID: 35154280, PMCID: PMC8831884, DOI: 10.3389/fgene.2022.820532.Peer-Reviewed Original ResearchMutant cell linesEpithelial-to-mesenchymal transitionCell linesGATA3 mutationsSplice site deletionLuminal breast cancer cell linesLuminal breast cancer cellsGene expression patternsMutant-expressing cellsBreast cancer cell linesMotif enrichmentChromatin localizationBreast cancer cellsMotif recognitionTruncation mutantsCancer cell linesSite deletionTranscriptome analysisTruncating mutationsBreast cancer developmentBreast cancer patientsBreast cancer characterizationRelated gene expressionMutated genesGene expression
2011
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M. Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. PLOS Computational Biology 2011, 7: e1002190. PMID: 22125477, PMCID: PMC3219617, DOI: 10.1371/journal.pcbi.1002190.Peer-Reviewed Original ResearchConceptsTranscription factorsRegulatory networksGenome-wide ChIP-seqIntegrated Regulatory NetworkHigh-throughput sequencing dataTargets of miRNAsProtein-protein interactionsMulti-level regulationRNA-seq dataRNA-seq profilesHigh-throughput datasetsSet of TFsModENCODE projectHigher eukaryotesC. elegansMotif enrichmentChIP-seqRegulatory interactionsHost genesTarget genesNegative regulatorSequencing dataMiRNAsNetwork motifsConservation information
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