2022
Cancer Relevance of Human Genes
Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal Of The National Cancer Institute 2022, 114: 988-995. PMID: 35417011, PMCID: PMC9275765, DOI: 10.1093/jnci/djac068.Peer-Reviewed Original ResearchConceptsCore cancer genesHuman genesFunctional importanceSomatic mutation frequencySelection pressureGene/protein networksCancer genesHigher somatic mutation frequencyNegative selection pressureGene-gene interaction networksMutation frequencyProtein-truncating variantsGenomic contextCell viabilityGenes decreasesCancer Genome AtlasInteraction networksProtein networkCancer relevanceCancer cell viabilityCell survivalGenesCancer biologyGenome AtlasSearch tools
2020
Early Modulation of Circulating MicroRNAs Levels in HER2-Positive Breast Cancer Patients Treated with Trastuzumab-Based Neoadjuvant Therapy
Di Cosimo S, Appierto V, Pizzamiglio S, Silvestri M, Baselga J, Piccart M, Huober J, Izquierdo M, de la Pena L, Hilbers FS, de Azambuja E, Untch M, Pusztai L, Pritchard K, Nuciforo P, Vincent-Salomon A, Symmans F, Apolone G, de Braud FG, Iorio MV, Verderio P, Daidone MG. Early Modulation of Circulating MicroRNAs Levels in HER2-Positive Breast Cancer Patients Treated with Trastuzumab-Based Neoadjuvant Therapy. International Journal Of Molecular Sciences 2020, 21: 1386. PMID: 32085669, PMCID: PMC7073028, DOI: 10.3390/ijms21041386.Peer-Reviewed Original ResearchConceptsPathological complete responseNeoadjuvant therapyHER2-positive breast cancer patientsTrastuzumab-based neoadjuvant therapyAvailable predictive biomarkersBreast cancer patientsEstrogen receptor statusComplete responseReceptor statusCancer patientsPredictive biomarkersTreatment responseHCC progressionPatientsPredictive valueBivariate analysisMean differencePlasma pairsTherapyEarly modulationMicroRNA levelsTrastuzumabMAPK signalingMetabolism regulationKEGG analysis
2014
Combined analysis of gene expression, DNA copy number, and mutation profiling data to display biological process anomalies in individual breast cancers
Shi W, Balazs B, Györffy B, Jiang T, Symmans WF, Hatzis C, Pusztai L. Combined analysis of gene expression, DNA copy number, and mutation profiling data to display biological process anomalies in individual breast cancers. Breast Cancer Research And Treatment 2014, 144: 561-568. PMID: 24619174, DOI: 10.1007/s10549-014-2904-z.Peer-Reviewed Original ResearchConceptsDNA copy numberBiological processesIndividual molecular eventsCopy numberGene expressionMolecular eventsMulticellular organismal processGene Ontology databaseGO biological processesSignal transduction pathwaysOrganismal processesGO termsMolecular dataTransduction pathwaysSiRNA screenComplex genomic abnormalitiesIndividual cancersOntology databaseFunctional roleDriver eventsCell growthSequence abnormalitiesBreast cancer cell linesCancer cell linesGenomic abnormalities
2012
A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes
Dutta B, Pusztai L, Qi Y, André F, Lazar V, Bianchini G, Ueno N, Agarwal R, Wang B, Shiang CY, Hortobagyi GN, Mills GB, Symmans WF, Balázsi G. A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. British Journal Of Cancer 2012, 106: 1107-1116. PMID: 22343619, PMCID: PMC3304402, DOI: 10.1038/bjc.2011.584.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsCell Line, TumorComputer SimulationDNA Copy Number VariationsEpithelial-Mesenchymal TransitionFemaleGene ExpressionGene Expression ProfilingGene Expression Regulation, NeoplasticGene Knockdown TechniquesGene Regulatory NetworksGenes, NeoplasmHumansModels, BiologicalProtein Interaction MapsReceptor, ErbB-2Receptors, EstrogenReceptors, ProgesteroneRNA InterferenceConceptsGenome-scale dataCore biological pathwaysTriple receptor-negative breast cancerProtein-protein interactionsCell line data setsGene knockdown experimentsGene copy number dataCopy number dataCopy number variation dataNumber variation dataMember genesGene networksTranscriptional disturbancesKnockdown experimentsBiological discoveryGene expressionFunctional specificityBiological pathwaysDifferential expressionIntegrative studyFunctional relevanceVariation dataLine data setsCell linesGenes
2009
Building Networks with Microarray Data
Broom BM, Rinsurongkawong W, Pusztai L, Do KA. Building Networks with Microarray Data. Methods In Molecular Biology 2009, 620: 315-343. PMID: 20652510, DOI: 10.1007/978-1-60761-580-4_10.Peer-Reviewed Original ResearchMeSH KeywordsAnalysis of VarianceBayes TheoremCluster AnalysisGene Expression ProfilingGene Regulatory NetworksHumansOligonucleotide Array Sequence AnalysisConceptsDetailed differential equation modelsDifferential equation modelAvailable breast cancer dataMathematical detailsNetwork modelBayesian network modelCo-expression network analysisMicroarray dataGene expression data setsFalse interactionsBayesian networkGene interaction networksData setsNumber of samplesPlausible networksRobust networkBreast cancer dataExpression data setsMicroarray data setsGene clusterGene shavingGene interactionsInteraction networksPreliminary clusteringSubsequent biological experiments