2017
Regulatory network changes between cell lines and their tissues of origin
Lopes-Ramos C, Paulson J, Chen C, Kuijjer M, Fagny M, Platig J, Sonawane A, DeMeo D, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics 2017, 18: 723. PMID: 28899340, PMCID: PMC5596945, DOI: 10.1186/s12864-017-4111-x.Peer-Reviewed Original ResearchConceptsLymphoblastoid cell linesCell linesTranscription factor (TFChIP-seq dataRegulatory network changesRNA-seq dataTissue of originRegulatory network analysisCell cycle genesPrimary tissuesGene expression analysisEpstein-Barr virus-transformed lymphoblastoid cell linesChIP-seqVirus-transformed lymphoblastoid cell linesTF-targetRNA-seqGTEx projectTF regulationCycle genesTranscriptomic differencesBackgroundCell linesTranscript levelsExpression analysisFibroblast cell lineNetwork analysis
2015
Elucidating Compound Mechanism of Action by Network Perturbation Analysis
Woo J, Shimoni Y, Yang W, Subramaniam P, Iyer A, Nicoletti P, Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell B, Bansal M, Califano A. Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Cell 2015, 162: 441-451. PMID: 26186195, PMCID: PMC4506491, DOI: 10.1016/j.cell.2015.05.056.Peer-Reviewed Original ResearchConceptsGenome-wide identificationRegulatory network analysisBind target proteinsCompound's mechanism of actionNovel proteinsTarget proteinsCompound perturbationGlobal dysregulationSmall molecule compoundsCompound similarityProteinNetwork-based approachRepair activityMolecular interactionsTested compoundsCompoundsMechanism of actionNetwork analysisCompound analysisActivity modulationAnticancer drugsCompound efficacyPerturbation profilesSimilarityEffector
2006
Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators
Keller MA, Addya S, Vadigepalli R, Banini B, Delgrosso K, Huang H, Surrey S. Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators. Physiological Genomics 2006, 28: 114-128. PMID: 16940433, DOI: 10.1152/physiolgenomics.00055.2006.Peer-Reviewed Original ResearchConceptsTranscriptional regulatory network analysisRegulatory network analysisTranscriptional regulatorsErythroid differentiation systemProbe setsCluster of genesPotential transcriptional regulatorsBlood cell lineagesDifferent expression patternsHuman erythroid progenitorsMRNA expression profilingBlood cell transcriptomeNetwork analysisErythroid developmentHematopoietic stem cellsCell transcriptomeDE genesTranscription factorsHematopoietic progenitor cellsEvi-1Target genesMolecular basisExpression profilingHuman erythropoiesisCell lineages
2005
Transcriptome Analysis of Human Hematopoietic Progenitor Cells during In Vitro Erythroid Differentiation.
Keller M, Addya S, Vadigepalli R, Ponte C, Banini B, Delgrosso K, Surrey S. Transcriptome Analysis of Human Hematopoietic Progenitor Cells during In Vitro Erythroid Differentiation. Blood 2005, 106: 1750. DOI: 10.1182/blood.v106.11.1750.1750.Peer-Reviewed Original ResearchTranscriptional regulatory elementsHematopoietic progenitor cellsHuman hematopoietic progenitor cellsDE genesTranscriptional regulatory network analysisTranscription factor occupancyGlobin gene expressionTranscriptional regulatory networksErythroid-specific genesTranscription factor interactionsAffymetrix Human Genome U133Different gene clustersRegulatory network analysisHuman erythroid cellsProgenitor cellsHuman Genome U133Presence of EpoMultiple cell typesFactor occupancyΓ-globin mRNAGene clusterGATA-1Transcriptome analysisHematopoietic stem cellsRegulatory networks
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