Protocol for identifying key genes using network-based approach as an alternative to differential expression analysis

Piyush Agrawal; Sridhar Hannenhalli

doi:10.1016/j.xpro.2024.103472

Protocol for identifying key genes using network-based approach as an alternative to differential expression analysis

STAR Protoc. 2024 Dec 20;5(4):103472. doi: 10.1016/j.xpro.2024.103472. Epub 2024 Dec 4.

Authors

Piyush Agrawal¹, Sridhar Hannenhalli²

Affiliations

¹ Department of Medical Research, SRM Medical College Hospital & Research Centre, SRMIST, Kattankulathur, Chennai, India. Electronic address: [email protected].
² Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA. Electronic address: [email protected].

Abstract

In a variety of biological contexts, characterizing genes associated with disease etiology and mediating global transcriptomic change is a key initial step. Here, we present a protocol to identify such key genes using our tool "PathExt," a tool that implements a network-based approach. We describe steps for installing libraries, preparing input data and detailed procedures for running PathExt, and characterizing differential pathways and key genes based on ripple centrality scores. For complete details on the use and execution of this protocol, please refer to Agrawal et al.¹^,².

Keywords: Bioinformatics; Cancer; Computer sciences; Genomics; Systems biology.

MeSH terms

Computational Biology / methods
Gene Expression Profiling* / methods
Gene Regulatory Networks* / genetics
Humans
Software
Transcriptome / genetics