Comprehensive Gene Expression Analysis and Identification of Stat-1 as Master Regulator in Oral Squamous Cell Carcinoma

1S.S. Ariya, Akhila Rachel James and Dr. Baby Joseph

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Abstract:

Gene expression profiling and analysis helps in identification of master regulators inducing disease. The GEO dataset GSE74530 comprising of samples from 6 normal and 6 oral cancer patients were analyzed using R package of Bio Conductor program GEO2R. The differentially expressed genes among the samples were identified using Benjamini Hochberg method. The up-regulated and down-regulated genes were identified based on fc value > 2.0 and p-value < 0.5. Protein interaction network was constructed for the up-regulated and down regulated genes with data from Bio Grid and Reactome database. The network was further explored by applying mathematical models for topological interaction analysis to determine the hub genes. Signal transducer and activator of transcription 1 (STAT1) was identified as the master regulator of Oral Squamous Cell Carcinoma (OSCC). Cross validation with The Cancer genome Atlas (TCGA) followed by gene ontology and functional enrichment analysis also revealed the role of STAT1 in progression of OSCC. Survival analysis with respect to expression of gene also showed the decrease in rate of patient prognosis with increase in expression of STAT1.

Keywords:

Oral Squamous Cell Carcinoma (OSCC), The Cancer Genome Atlas.

Paper Details
Month3
Year2020
Volume24
IssueIssue 5
Pages399-417