2025
A Selective Review of Network Analysis Methods for Gene Expression Data
Li R, Yi H, Ma S. A Selective Review of Network Analysis Methods for Gene Expression Data. Methods In Molecular Biology 2025, 2880: 293-307. PMID: 39900765, DOI: 10.1007/978-1-0716-4276-4_14.Peer-Reviewed Original ResearchConceptsGene expression dataGene expression networksExpression dataDownstream analysisExpression networksGene expressionBiological processesGenesMolecular mechanismsBiological implicationsHigh-throughput profiling techniquesBiological findingsGlobal viewComplex interactionsProfiling techniquesRegulation
2024
The dynamics of hematopoiesis over the human lifespan
Li H, Côté P, Kuoch M, Ezike J, Frenis K, Afanassiev A, Greenstreet L, Tanaka-Yano M, Tarantino G, Zhang S, Whangbo J, Butty V, Moiso E, Falchetti M, Lu K, Connelly G, Morris V, Wang D, Chen A, Bianchi G, Daley G, Garg S, Liu D, Chou S, Regev A, Lummertz da Rocha E, Schiebinger G, Rowe R. The dynamics of hematopoiesis over the human lifespan. Nature Methods 2024, 22: 422-434. PMID: 39639169, PMCID: PMC11908799, DOI: 10.1038/s41592-024-02495-0.Peer-Reviewed Original ResearchConceptsHematopoietic stem cellsHematopoietic stemProgenitor cellsClassification of acute myeloid leukemiaDifferentiation of hematopoietic stem cellsAssociated with poor prognosisAcute myeloid leukemiaHuman hematopoietic stemWave of hematopoiesisGene expression networksMyeloid leukemiaPoor prognosisLineage outputMultilineage capacityDynamics of hematopoiesisCell ontogenyStem cellsLineage primingFate decisionsModel organismsTranscriptomic statesExpression networksHuman lifespanTranscriptional programsHematopoiesisIncorporating prior information in gene expression network-based cancer heterogeneity analysis
Li R, Xu S, Li Y, Tang Z, Feng D, Cai J, Ma S. Incorporating prior information in gene expression network-based cancer heterogeneity analysis. Biostatistics 2024, 26: kxae028. PMID: 39074174, DOI: 10.1093/biostatistics/kxae028.Peer-Reviewed Original Research
2020
Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis
VanOudenhove J, Yankee T, Wilderman A, Cotney J. Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis. Circulation Research 2020, 127: e184-e209. PMID: 32772801, PMCID: PMC7554226, DOI: 10.1161/circresaha.120.316704.Peer-Reviewed Original ResearchMeSH KeywordsChromatinEnhancer Elements, GeneticEpigenomicsGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenetic VariationHeartHeart Defects, CongenitalHistone CodeHomeobox Protein Nkx-2.5HumansNAV1.5 Voltage-Gated Sodium ChannelOrganogenesisRegulatory Sequences, Ribonucleic AcidT-Box Domain ProteinsTranscriptomeConceptsRegulatory sequencesHeart enhancersHeart organogenesisGene expression network analysisWeighted gene coexpression networkGene expression dynamicsGene expression networksPutative disease genesWhole-genome sequencing dataGene coexpression networksExpression network analysisDisease-relevant genesGenome sequencing dataRare sequence alterationsHeart-specific expressionClear genetic componentChromatin stateTranscriptomic dynamicsHistone modificationsFunctional annotationExpression networksExpression dynamicsGene modulesCoexpression networkGenetic variation
2019
Transcriptional regulatory model of fibrosis progression in the human lung
McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight 2019, 4 PMID: 31600171, PMCID: PMC6948862, DOI: 10.1172/jci.insight.131597.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAdvanced fibrosisAlveolar surface densityFibrosis progressionLung fibrosisHuman lungDynamic Regulatory Events MinerExtent of fibrosisIPF lungsPulmonary fibrosisControl lungsIPF tissueB lymphocytesFibrosisLungLinear mixed-effects modelsMixed-effects modelsGene expression changesSystems biology modelsDifferential gene expression analysisGene expression analysisProgressionGene expression networksRNA sequencingBiology models
2016
Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease
Modena BD, Bleecker ER, Busse WW, Erzurum SC, Gaston BM, Jarjour NN, Meyers DA, Milosevic J, Tedrow JR, Wu W, Kaminski N, Wenzel SE. Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease. American Journal Of Respiratory And Critical Care Medicine 2016, 195: 1449-1463. PMID: 27984699, PMCID: PMC5470748, DOI: 10.1164/rccm.201607-1407oc.Peer-Reviewed Original ResearchConceptsWeighted gene coexpression network analysisGene coexpression network analysisCoexpression network analysisGene expressionBiological processesAirway epithelial cell gene expressionEpithelial cell gene expressionNetwork of genesGene expression networksGene network modulesAsthma susceptibility lociT2 gene expressionCell gene expressionGene expression studiesNeuronal functionEpithelial growthMultiple molecular mechanismsExpression networksT2 genesGene networksUnderlying biological processesHub genesExpression studiesBiological insightsNetwork analysisDeconstructing Olfaction with Transcriptomics: From Whole Tissue to Single-Cells, and from Zebrafish to Humans
Saraiva L, Ibarra-Soria X, Aguilera F, Marioni J, Logan D. Deconstructing Olfaction with Transcriptomics: From Whole Tissue to Single-Cells, and from Zebrafish to Humans. 2016 DOI: 10.5339/qfarc.2016.hbpp2867.Peer-Reviewed Original ResearchOlfactory sensory neuronsFluorescence assisted cell sortingMature olfactory sensory neuronsMolecular barcodesOlfactory receptorsDegree of molecular conservationOlfactory mucosaCell type-specific genesDynamics of gene expressionInter-specific levelType-specific genesOR gene repertoireSingle-cellGene expression networksOlfactory systemEvolution of olfactionMolecular heterogeneityPopulation of olfactory sensory neuronsCilia of olfactory sensory neuronsReceptive matesSpecies nichesMolecular conservationRNA-seqGene familyGene repertoire
2013
Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies
Hou L, Chen M, Zhang CK, Cho J, Zhao H. Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies. Human Molecular Genetics 2013, 23: 2780-2790. PMID: 24381306, PMCID: PMC3990172, DOI: 10.1093/hmg/ddt668.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesWide association studyDisease-associated genesGWAS signalsNetwork rewiringAssociation studiesFunctional genomic informationGene expression networksCo-expression networkDisease-associated pathwaysExpression networksGene networksGenomic informationAssociation signalsGene prioritizationDisease genesDisease locusSusceptibility lociGenesAssociation principleRewiringDisease associationsLociMillions of candidatesDisease conditions
2012
Reshaping of global gene expression networks and sex‐biased gene expression by integration of a young gene
Chen S, Ni X, Krinsky BH, Zhang YE, Vibranovski MD, White KP, Long M. Reshaping of global gene expression networks and sex‐biased gene expression by integration of a young gene. The EMBO Journal 2012, 31: 2798-2809. PMID: 22543869, PMCID: PMC3380208, DOI: 10.1038/emboj.2012.108.Peer-Reviewed Original ResearchConceptsSex-biased gene expressionNew genesGene expressionPre-existing genesCo-evolved interactionsGenomic binding profileNew gene networksComparative expression profilingOrgan expression patternsGene expression networksEssential biological processesDiverse taxaYoung genesExpression networksGene networksRelated speciesGenetic networksDownstream genesGenomic levelExpression profilingExpression patternsBiological processesGenesMale fecundityCAF40
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