2017
GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles
Klein MI, Stern DF, Zhao H. GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics 2017, 18: 317. PMID: 28651562, PMCID: PMC5485588, DOI: 10.1186/s12859-017-1711-z.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression ProfilingHumansInternetNeoplasmsSupport Vector MachineSurvival AnalysisTranscriptomeUser-Computer InterfaceConceptsGene expression profilesExpression profilesIndividual gene expression profilesTissue-specific functionalityEnrichment-based methodsPathway scoresGene expression levelsBatch effectsPathway genesPresent genesPerturbed pathwaysPathway expressionExpression levelsIndividual samplesTissue typesPathwayGenesTCGA subtypesAbnormal pathwaysIndependent datasetsBreast cancer subtypesNon-competitive approachIndividual tumorsCancer subtypesGrapes
2016
Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival – Evidence from TCGA Pan-Cancer Data
Huang X, Stern DF, Zhao H. Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival – Evidence from TCGA Pan-Cancer Data. Scientific Reports 2016, 6: 20567. PMID: 26837275, PMCID: PMC4738355, DOI: 10.1038/srep20567.Peer-Reviewed Original ResearchConceptsPatient survivalTumor cell contaminationField cancerization effectNormal samplesCancer patient survivalNormal tissue samplesSitu immunizationCancer Genome AtlasCancer patientsPatient progressionNormal controlsTumorsNormal tissuesPan-cancer dataTissue samplesGenome AtlasCancer studiesDisease etiologyCell contaminationPatientsPathway analysisTCGA pan-cancer dataSurvivalTranscriptional profilesPotential benefitsPMCA2 regulates HER2 protein kinase localization and signaling and promotes HER2-mediated breast cancer
Jeong J, VanHouten JN, Dann P, Kim W, Sullivan C, Yu H, Liotta L, Espina V, Stern DF, Friedman PA, Wysolmerski JJ. PMCA2 regulates HER2 protein kinase localization and signaling and promotes HER2-mediated breast cancer. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e282-e290. PMID: 26729871, PMCID: PMC4725473, DOI: 10.1073/pnas.1516138113.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBreast NeoplasmsCalciumCarcinogenesisCell Line, TumorCell MembraneCell ProliferationCell SurvivalEndocytosisFemaleFluorescent Antibody TechniqueForkhead Box Protein O1Forkhead Transcription FactorsGene Knockdown TechniquesHSP90 Heat-Shock ProteinsHumansImmunoblottingIntracellular SpaceMammary Neoplasms, AnimalMicePlasma Membrane Calcium-Transporting ATPasesProtein BindingProtein TransportReceptor, ErbB-2Signal TransductionSurvival AnalysisConceptsBreast cancerHigh tumor levelsDegradation of HER2Increases Intracellular CalciumMouse mammary tumor virusBreast cancer cellsMammary tumor virusPMCA2 levelsNeu miceTumor levelsFormation of tumorsHER2 levelsIntracellular calciumTherapeutic targetBreast tumorsHER2Milk calciumExpression correlatesCancerHSP 90Mammary glandCancer cellsTumor virusTumorsCalcium
2005
Relationship of Epidermal Growth Factor Receptor Expression to ErbB-2 Signaling Activity and Prognosis in Breast Cancer Patients
DiGiovanna MP, Stern DF, Edgerton SM, Whalen SG, Moore D, Thor AD. Relationship of Epidermal Growth Factor Receptor Expression to ErbB-2 Signaling Activity and Prognosis in Breast Cancer Patients. Journal Of Clinical Oncology 2005, 23: 1152-1160. PMID: 15718311, DOI: 10.1200/jco.2005.09.055.Peer-Reviewed Original ResearchConceptsEpidermal growth factor receptor expressionGrowth factor receptor expressionBreast cancer patientsBreast cancerHuman breast cancerFactor receptor expressionErbB-2Cancer patientsReceptor expressionEGFR expressionEarly-stage breast cancerAdverse prognostic valueErbB-2 phosphorylationFirst clinical evidenceInvasive breast cancerPrognosis of patientsPercent of tumorsParaffin tumor sectionsErbB-2 activationErbB-2 overexpressionLigand-dependent mechanismTreatment of tumorsClinical evidencePrognostic valueShorter survival
2000
Activation (tyrosine phosphorylation) of ErbB-2 (HER-2/neu): a study of incidence and correlation with outcome in breast cancer.
Thor AD, Liu S, Edgerton S, Moore D, Kasowitz KM, Benz CC, Stern DF, DiGiovanna MP. Activation (tyrosine phosphorylation) of ErbB-2 (HER-2/neu): a study of incidence and correlation with outcome in breast cancer. Journal Of Clinical Oncology 2000, 18: 3230-9. PMID: 10986055, DOI: 10.1200/jco.2000.18.18.3230.Peer-Reviewed Original ResearchConceptsBreast cancerErbB-2 expressionPrognostic valueErbB-2Node-positive breast cancerNode-positive patientsPositive lymph nodesDisease-specific survivalPrimary breast cancerAdditional prognostic valueInvasive breast cancerNode-positive casesBreast cancer patientsSignificant prognostic valueStudy of incidenceArchival breast cancer samplesErbB-2-positive cellsBreast cancer samplesBreast cancer cellsInvasive breast cancer cellsIdentification of casesLymph nodesPatient groupPoor prognosisCancer patients