2019
Global gene expression of histologically normal primary skin cells from BCNS subjects reveals “single-hit” effects that are influenced by rapamycin
Phatak A, Athar M, Crowell JA, Leffel D, Herbert BS, Bale AE, Kopelovich L. Global gene expression of histologically normal primary skin cells from BCNS subjects reveals “single-hit” effects that are influenced by rapamycin. Oncotarget 2019, 10: 1360-1387. PMID: 30858923, PMCID: PMC6402716, DOI: 10.18632/oncotarget.26640.Peer-Reviewed Original ResearchGlobal gene expressionRapamycin treatmentGene expression changesGene expression profilingPresence of rapamycinBiomarkers/targetsExpression profilingGene expressionExpression changesPrimary cell culturesWnt pathwayCanonical HhGenesProbe setsMitochondrial dysfunctionStellate cell activationUnaffected skin biopsiesHeritable cancersPrimary skin cellsStem cellsRapamycinDevelopmental abnormalitiesDifferential responseGene signatureNormal fibroblasts
2016
Comparative mRNA analysis of behavioral and genetic mouse models of aggression
Malki K, Tosto MG, Pain O, Sluyter F, Mineur YS, Crusio WE, de Boer S, Sandnabba KN, Kesserwani J, Robinson E, Schalkwyk LC, Asherson P. Comparative mRNA analysis of behavioral and genetic mouse models of aggression. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2016, 171: 427-436. PMID: 26888158, DOI: 10.1002/ajmg.b.32424.Peer-Reviewed Original ResearchConceptsProbe setsExpression of genesGenetic mouse studiesGene hubsGene networksProtein degradationCandidate genesERG2 geneNetwork analysisGenetic mouse modelsDiscovery-replication designRedox pathwaysGenesP38 MAPKAggression-related traitsMouse modelMouse brain tissueGenetic modelsMRNA studiesMRNA analysisDiscovery studiesDiscovery setPathwayMouse studiesSignificant overlap
2007
Evaluation of the feasibility of expression microarray analysis in endoscopically obtained biopsies of gastric carcinoma and their clinical applicability
Jhawer M, Qin L, Gerdes H, Klimstra D, Schattner M, Viale A, Gonen M, Schwartz G, Kelsen D, Shah M. Evaluation of the feasibility of expression microarray analysis in endoscopically obtained biopsies of gastric carcinoma and their clinical applicability. Journal Of Clinical Oncology 2007, 25: 21164-21164. DOI: 10.1200/jco.2007.25.18_suppl.21164.Peer-Reviewed Original ResearchEndoscopic biopsyExpression microarray analysisGastric cancerLauren classificationGastric carcinomaGene expression profilesMicroarray analysisExpression analysisGastroesophageal junction adenocarcinomaFresh tumor tissueDiffuse gastric cancerNCI-sponsored trialsExpression profilesThreshold p <Probe setsLauren histologyJunction adenocarcinomaPathology reviewTumor specimensCisplatin chemotherapyDifferential gene expression profilesGene probe setsTumor tissuesIntestinal-typeBiopsyGene expression profile of ovarian serous papillary carcinomas: identification of metastasis-associated genes
Bignotti E, Tassi RA, Calza S, Ravaggi A, Bandiera E, Rossi E, Donzelli C, Pasinetti B, Pecorelli S, Santin AD. Gene expression profile of ovarian serous papillary carcinomas: identification of metastasis-associated genes. American Journal Of Obstetrics And Gynecology 2007, 196: 245.e1-245.e11. PMID: 17346539, DOI: 10.1016/j.ajog.2006.10.874.Peer-Reviewed Original ResearchConceptsMetastasis-associated genesGene expressionOverexpression of CXCL12Gene expression profilesGene expression profilingMetastatic ovarian cancerNumber of invasionsHepsin geneHuman genesExpression profilingExpression profilesOligonucleotide microarraysQuantitative real-time polymerase chain reactionOvarian cancerGenesProbe setsPrimary ovarian serous carcinomaOvarian serous papillary carcinomaSerous papillary ovarian carcinomasProtein levelsSerous papillary carcinomaReal-time polymerase chain reactionOvarian serous carcinomaOspCPredictive genes
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
Gene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis
Selman M, Pardo A, Barrera L, Estrada A, Watson SR, Wilson K, Aziz N, Kaminski N, Zlotnik A. Gene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis. American Journal Of Respiratory And Critical Care Medicine 2005, 173: 188-198. PMID: 16166619, PMCID: PMC2662988, DOI: 10.1164/rccm.200504-644oc.Peer-Reviewed Original ResearchConceptsGene expression signaturesExpression signaturesCustom oligonucleotide microarrayGene expression patternsOligonucleotide DNA microarrayStandard Affymetrix protocolGene clusterDNA microarraysExpression patternsGene expressionOligonucleotide microarraysComplementary ribonucleic acidTranscriptional signatureProbe setsCustom arrayT cell activationTissue remodelingNonspecific interstitial pneumoniaRibonucleic acidGenesMicroarrayInterstitial lung diseaseHypersensitivity pneumonitisPathogenic mechanismsExpression
2004
Gene expression profiles in primary ovarian serous papillary tumors and normal ovarian epithelium: Identification of candidate molecular markers for ovarian cancer diagnosis and therapy
Santin AD, Zhan F, Bellone S, Palmieri M, Cane S, Bignotti E, Anfossi S, Gokden M, Dunn D, Roman JJ, O'Brien TJ, Tian E, Cannon MJ, Shaughnessy J, Pecorelli S. Gene expression profiles in primary ovarian serous papillary tumors and normal ovarian epithelium: Identification of candidate molecular markers for ovarian cancer diagnosis and therapy. International Journal Of Cancer 2004, 112: 14-25. PMID: 15305371, DOI: 10.1002/ijc.20408.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBiomarkers, TumorCarcinoma, PapillaryCells, CulturedCystadenocarcinoma, SerousEpitheliumFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMiddle AgedOligonucleotide Array Sequence AnalysisOvarian NeoplasmsOvaryReverse Transcriptase Polymerase Chain ReactionRNA, MessengerSerine EndopeptidasesConceptsGene expression profilesExpression profilesOvarian serous papillary carcinomaExpression dataDifferential expressionTumor-associated calcium signal transducer 1Cell linesGrowth factor beta receptor IIINormal ovarian epitheliumPlatelet-derived growth factor receptor alphaGene expression dataGrowth factor receptor alphaCandidate molecular markersOvarian epitheliumGene expressionLadinin-1Oligonucleotide microarraysMolecular markersQuantitative RT-PCRGenesClaudin-3Probe setsOvarian cancerClaudin-4Important molecular featuresDiscrimination between uterine serous papillary carcinomas and ovarian serous papillary tumours by gene expression profiling
Santin AD, Zhan F, Bellone S, Palmieri M, Cane S, Gokden M, Roman JJ, O'Brien TJ, Tian E, Cannon MJ, Shaughnessy J, Pecorelli S. Discrimination between uterine serous papillary carcinomas and ovarian serous papillary tumours by gene expression profiling. British Journal Of Cancer 2004, 90: 1814-1824. PMID: 15208622, PMCID: PMC2409747, DOI: 10.1038/sj.bjc.6601791.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedCarcinoma, PapillaryCells, CulturedCystadenocarcinoma, SerousDiagnosis, DifferentialFemaleFlow CytometryGene Expression ProfilingGene Expression Regulation, NeoplasticHumansImmunohistochemistryMiddle AgedOligonucleotide Array Sequence AnalysisOvarian NeoplasmsReceptor, ErbB-2Reverse Transcriptase Polymerase Chain ReactionUterine NeoplasmsConceptsUterine serous papillary carcinomaGene expressionOverexpressed genesSerous papillary carcinomaGene expression fingerprintGene expression profilingHuman genesC-erbB2 geneExpression fingerprintsMolecular basisExpression profilingPapillary carcinomaOligonucleotide microarraysExpression productsQuantitative RT-PCRGenesClinical tissue samplesProbe setsTwo-fold differenceMore effective treatment modalitiesEffective treatment modalitySerous papillary tumorsPlasminogen activator inhibitorDifferent biological behaviorDevelopment of novel
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