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Research article - Peer-reviewed, 2021

Transcriptome profiling by combined machine learning and statistical R analysis identifies TMEM236 as a potential novel diagnostic biomarker for colorectal cancer

Maurya, Neha Shree; Kushwaha, Sandeep; Chawade, Aakash; Mani, Ashutosh

Abstract

Colorectal cancer (CRC) is a common cause of cancer-related deaths worldwide. The CRC mRNA gene expression dataset containing 644 CRC tumor and 51 normal samples from the cancer genome atlas (TCGA) was pre-processed to identify the significant differentially expressed genes (DEGs). Feature selection techniques Least absolute shrinkage and selection operator (LASSO) and Relief were used along with class balancing for obtaining features (genes) of high importance. The classification of the CRC dataset was done by ML algorithms namely, random forest (RF), K-nearest neighbour (KNN), and artificial neural networks (ANN). The significant DEGs were 2933, having 1832 upregulated and 1101 downregulated genes. The CRC gene expression dataset had 23,186 features. LASSO had performed better than Relief for classifying tumor and normal samples through ML algorithms namely RF, KNN, and ANN with an accuracy of 100%, while Relief had given 79.5%, 85.05%, and 100% respectively. Common features between LASSO and DEGs were 38, from them only 5 common genes namely, VSTM2A, NR5A2, TMEM236, GDLN, and ETFDH had shown statistically significant survival analysis. Functional review and analysis of the selected genes helped in downsizing the 5 genes to 2, which are VSTM2A and TMEM236. Differential expression of TMEM236 was statistically significant and was markedly reduced in the dataset which solicits appreciation for assessment as a novel biomarker for CRC diagnosis.

Published in

Scientific Reports
2021, volume: 11, number: 1, article number: 14304
Publisher: NATURE RESEARCH

Authors' information

Maurya, Neha Shree
National Institute of Technology (NIT System)
Kushwaha, Sandeep
National Institute of Animal Biotechnology (NIAB)
Swedish University of Agricultural Sciences, Department of Plant Breeding
Mani, Ashutosh
National Institute of Technology (NIT System)

UKÄ Subject classification

Medical Genetics

Publication Identifiers

DOI: https://doi.org/10.1038/s41598-021-92692-0

URI (permanent link to this page)

https://res.slu.se/id/publ/113234