Identification of molecular biomarkers and pathways of NSCLC: insights from a systems biomedicine perspective

Rakibul Islam, Liton Ahmed, Bikash Kumar Paul, Kawsar Ahmed, Touhid Bhuiyan, Mohammad Ali Moni

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Worldwide, more than 80% of identified lung cancer cases are associated to the non-small cell lung cancer (NSCLC). We used microarray gene expression dataset GSE10245 to identify key biomarkers and associated pathways in NSCLC. Results: To collect Differentially Expressed Genes (DEGs) from the dataset GSE10245, we applied the R statistical language. Functional analysis was completed using the Database for Annotation Visualization and Integrated Discovery (DAVID) online repository. The DifferentialNet database was used to construct Protein–protein interaction (PPI) network and visualized it with the Cytoscape software. Using the Molecular Complex Detection (MCODE) method, we identify clusters from the constructed PPI network. Finally, survival analysis was performed to acquire the overall survival (OS) values of the key genes. One thousand eighty two DEGs were unveiled after applying statistical criterion. Functional analysis showed that overexpressed DEGs were greatly involved with epidermis development and keratinocyte differentiation; the under-expressed DEGs were principally associated with the positive regulation of nitric oxide biosynthetic process and signal transduction. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway investigation explored that the overexpressed DEGs were highly involved with the cell cycle; the under-expressed DEGs were involved with cell adhesion molecules. The PPI network was constructed with 474 nodes and 2233 connections. Conclusions: Using the connectivity method, 12 genes were considered as hub genes. Survival analysis showed worse OS value for SFN, DSP, and PHGDH. Outcomes indicate that Stratifin may play a crucial role in the development of NSCLC.
Original languageEnglish
Pages (from-to)43
JournalJournal of Genetic Engineering and Biotechnology
Volume19
Issue number1
DOIs
Publication statusPublished - 19 Mar 2021
Externally publishedYes

Keywords

  • Gene expression
  • Gene ontology
  • KEGG pathway analysis
  • Molecular biomarkers
  • PPI network

Fingerprint

Dive into the research topics of 'Identification of molecular biomarkers and pathways of NSCLC: insights from a systems biomedicine perspective'. Together they form a unique fingerprint.

Cite this