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Differential gene expression and network analysis in head and neck squamous cell carcinoma

journal contribution
posted on 2023-05-21, 05:47 authored by Habib, I, Anjum, F, Mohammad, T, Sulaimani, MN, Shafie, A, Almehmadi, M, Yadav, DK, Sukhwinder SohalSukhwinder Sohal, Hassan, MI
Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignancy with a poor prognosis, whose biomarkers have not been studied in great detail. We have collected genomic data of HNSCC patients from The Cancer Genome Atlas (TCGA) and analyzed them to get deeper insights into the gene expression pattern. Initially, 793 differentially expressed genes (DEGs) were categorized, and their enrichment analysis was performed. Later, a protein–protein interaction network for the DEGs was constructed using the STRING plugin in Cytoscape to study their interactions. A set of 10 hub genes was selected based on Maximal Clique Centrality score, and later their survival analysis was studied. The elucidated set of 10 genes, i.e., PRAME, MAGEC2, MAGEA12, LHX1, MAGEA3, CSAG1, MAGEA6, LCE6A, LCE2D, LCE2C, referred to as potential candidates to be explored as HNSCC biomarkers. The Kaplan–Meier overall survival of the selected genes suggested that the alterations in the candidate genes were linked to the decreased survival of the HNSCC patients. Altogether, the results of this study signify that the genomic alterations and differential expression of the selected genes can be explored in therapeutic interpolations of HNSCC, exploiting early diagnosis and target-propelled therapy.


Publication title

Molecular and Cellular Biochemistry










School of Health Sciences


Kluwer Academic Publ

Place of publication

Van Godewijckstraat 30, Dordrecht, Netherlands, 3311 Gz

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© 2022 The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature

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Socio-economic Objectives

Diagnosis of human diseases and conditions

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