Kumar N, Mishra B, Mukhtar MS. A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions.
STAR Protoc 2022;
3:101608. [PMID:
35990739 PMCID:
PMC9386103 DOI:
10.1016/j.xpro.2022.101608]
[Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Investigating the complexity of host-pathogen interactions is challenging. Here, we outline a pipeline to identify important proteins and signaling molecules in human-viral interactomes. Firstly, we curate a comprehensive human interactome. Subsequently, we infer viral targets and transcriptome-specific human interactomes (VTTSHI) for papillomavirus and herpes viruses by integrating viral targets and transcriptome data. Finally, we reveal the common and shared nodes and pathways in viral pathogenesis following network topology and pathway enrichment analyses.
For complete details on the use and execution of this protocol, please refer to Kumar et al. (2020).
Protocol for integrative analysis of transcriptome and proteome network data
Network subgroup enrichment of two host-pathogen interaction networks
Preprocessing of data and heterogeneous network integration
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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