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dc.contributor.authorOchs, Michael F.
dc.contributor.authorStansfield, John C.
dc.contributor.authorRusay, Matthew
dc.contributor.authorShan, Roger
dc.contributor.authorKelton, Conor
dc.contributor.authorGaykalova, Daria A.
dc.contributor.authorFertig, Elana J.
dc.contributor.authorCalifano, Joseph A.
dc.date.accessioned2018-04-21T15:41:49Z
dc.date.available2018-04-21T15:41:49Z
dc.date.issued2016
dc.identifier.citationJohn C., S., Matthew, R., Roger, S., Conor, K., Daria A., G., Elana J., F., & ... Michael F., O. (2016). Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination. Cancer Informatics, Vol 2016, Iss 15, Pp 15-21 (2016), (15), 15.en_US
dc.identifier.urihttps://dx.doi.org/10.4137/CIN.S32468
dc.description.abstractThe goal of this study was to discover a minimally invasive pathway-specific biomarker that is immune to normal cell mRNA contamination for diagnosing head and neck squamous cell carcinoma (HNSCC). Using Elsevier's MedScan natural language processing component of the Pathway Studio software and the TRANSFAC database, we produced a curated set of genes regulated by the signaling networks driving the development of HNSCC. The network and its gene targets provided prior probabilities for gene expression, which guided our CoGAPS matrix factorization algorithm to isolate patterns related to HNSCC signaling activity from a microarray-based study. Using patterns that distinguished normal from tumor samples, we identified a reduced set of genes to analyze with Top Scoring Pair in order to produce a potential biomarker for HNSCC. Our proposed biomarker comprises targets of the transcription factor (TF) HIF1A and the FOXO family of TFs coupled with genes that show remarkable stability across all normal tissues. Based on validation with novel data from The Cancer Genome Atlas (TCGA), measured by RNAseq, and bootstrap sampling, the biomarker for normal vs. tumor has an accuracy of 0.77, a Matthews correlation coefficient of 0.54, and an area under the curve (AUC) of 0.82.en_US
dc.language.isoen_USen_US
dc.publisherLibertas Academicaen_US
dc.subjectgene expression profilingen_US
dc.subjectbiomarkersen_US
dc.subjectcanceren_US
dc.subjectbiostatisticsen_US
dc.titleToward Signaling-Driven Biomarkers Immune to Normal Tissue Contaminationen_US
dc.typeArticleen_US
dc.typeTexten_US
prism.publicationNameCancer Informatics
prism.volume15
prism.publicationDate2016
dc.identifier.handlehttps://dr.tcnj.edu/handle/2900/2279


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