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 ResearchConceptsGene 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 benefits