2020
Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues
Lopes-Ramos C, Chen C, Kuijjer M, Paulson J, Sonawane A, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo D. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports 2020, 31: 107795. PMID: 32579922, PMCID: PMC7898458, DOI: 10.1016/j.celrep.2020.107795.Peer-Reviewed Original ResearchConceptsGene regulatory networksTranscription factorsGenotype-Tissue ExpressionRegulatory networksArchitecture of gene regulatory networksRepertoire of transcription factorsSets of transcription factorsRegulatory network structureWhole-genome expression profilingTissue-related functionsGenes associated with Parkinson's diseaseHuman healthy tissuesGene regulationGene expressionMolecular basisSystems-based analysisExpression profilesGenesAlzheimer's diseaseRegulatory processesHuman tissuesExpressionTranscriptionTissueSex differences
2017
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Paulson J, Chen C, Lopes-Ramos C, Kuijjer M, Platig J, Sonawane A, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics 2017, 18: 437. PMID: 28974199, PMCID: PMC5627434, DOI: 10.1186/s12859-017-1847-x.Peer-Reviewed Original ResearchConceptsRNA-seq data setsRNA-seqGenotype-Tissue ExpressionRNA-seq processingGenome-wide transcriptional profilingRNA-seq studiesRNA-seq dataGene filteringDownstream analysisRNA sequencingTranscriptional profilesDiverse tissuesAnalytical pipelineR packageQuality controlSignificant analytical challengeSoftware pipelineGenesRNAMulti-group studyNormalization stepAnalytical challengesResultsWeTissueExpressionUnderstanding Tissue-Specific Gene Regulation
Sonawane A, Platig J, Fagny M, Chen C, Paulson J, Lopes-Ramos C, DeMeo D, Quackenbush J, Glass K, Kuijjer M. Understanding Tissue-Specific Gene Regulation. Cell Reports 2017, 21: 1077-1088. PMID: 29069589, PMCID: PMC5828531, DOI: 10.1016/j.celrep.2017.10.001.Peer-Reviewed Original ResearchConceptsTissue specificityTissue-specific gene regulationGenotype-Tissue Expression projectControl tissue specificityTissue-specific genesTranscription factor targetsTissue-specific functionsGene expression patternsGene set enrichment analysisTissue-specific mannerTissue-specific processesInvestigate gene expressionGene regulationRegulatory interactionsTranscriptional controlTranscription factor expressionTranscription factorsExpression projectEnrichment analysisGene expressionExpression patternsGenesRegulation nodeFactor targetsTranscriptionExploring regulation in tissues with eQTL networks
Fagny M, Paulson J, Kuijjer M, Sonawane A, Chen C, Lopes-Ramos C, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e7841-e7850. PMID: 28851834, PMCID: PMC5604022, DOI: 10.1073/pnas.1707375114.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociEQTL networksGenetic variantsCoherent biological processesImpact of genetic variantsActive chromatin regionsQuantitative trait lociTissue-specific processesGene expression levelsChromatin regionsGroup genesTrait lociComplex phenotypesRegulatory potentialGenotype to phenotype mappingPhenotype mappingBiological processesRegulatory functionsExpression levelsGenesRegulatory impactVariantsLociBipartite networksPhenotype
2015
Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine
Carrillo J, He Y, Luo J, Menendez K, Tablante N, Zhao K, Paulson J, Li B, Song J. Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine. PLOS ONE 2015, 10: e0100476. PMID: 26107953, PMCID: PMC4481310, DOI: 10.1371/journal.pone.0100476.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChickensCpG IslandsDNA MethylationEukaryotic Initiation Factor-2Gene Regulatory NetworksGenomeHerpesvirus 1, GallidImmune System DiseasesInflammationRibosomal Protein S6 Kinases, 70-kDaRNA Processing, Post-TranscriptionalSignal TransductionTOR Serine-Threonine KinasesTranscription Initiation SiteVaccinesConceptsTranscription start siteMethyl-CpG binding domain protein-enriched genome sequencingDNA methylationProtein-enriched genome sequencingRNA post-transcriptional modificationsIdentified canonical pathwaysRegulation of eIF4Post-transcriptional modificationsDifferentially expressed genesAxonal guidance signalingGlobal DNA methylationHypermethylated DMRsP70S6K signalingGenome sequenceStart siteMethylome analysisCpG islandsGene networksMethyl-CpGEIF2 signalingCanonical pathwaysK signalingGenesMTOR signalingInfectious laryngotracheitis