A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions
Summary: 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 transcrip...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-09-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722004889 |
| _version_ | 1811315520034570240 |
|---|---|
| author | Nilesh Kumar Bharat Mishra M. Shahid Mukhtar |
| author_facet | Nilesh Kumar Bharat Mishra M. Shahid Mukhtar |
| author_sort | Nilesh Kumar |
| collection | DOAJ |
| description | Summary: 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). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-13T11:31:34Z |
| format | Article |
| id | doaj.art-34335492240d4d77a222830f6bdc43e8 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-13T11:31:34Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-34335492240d4d77a222830f6bdc43e82022-12-22T02:48:33ZengElsevierSTAR Protocols2666-16672022-09-0133101608A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactionsNilesh Kumar0Bharat Mishra1M. Shahid Mukhtar2Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USADepartment of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USADepartment of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Corresponding authorSummary: 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). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722004889BioinformaticsGenomicsImmunologyMicrobiologySystems biology |
| spellingShingle | Nilesh Kumar Bharat Mishra M. Shahid Mukhtar A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions STAR Protocols Bioinformatics Genomics Immunology Microbiology Systems biology |
| title | A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions |
| title_full | A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions |
| title_fullStr | A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions |
| title_full_unstemmed | A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions |
| title_short | A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions |
| title_sort | pipeline of integrating transcriptome and interactome to elucidate central nodes in host pathogens interactions |
| topic | Bioinformatics Genomics Immunology Microbiology Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722004889 |
| work_keys_str_mv | AT nileshkumar apipelineofintegratingtranscriptomeandinteractometoelucidatecentralnodesinhostpathogensinteractions AT bharatmishra apipelineofintegratingtranscriptomeandinteractometoelucidatecentralnodesinhostpathogensinteractions AT mshahidmukhtar apipelineofintegratingtranscriptomeandinteractometoelucidatecentralnodesinhostpathogensinteractions AT nileshkumar pipelineofintegratingtranscriptomeandinteractometoelucidatecentralnodesinhostpathogensinteractions AT bharatmishra pipelineofintegratingtranscriptomeandinteractometoelucidatecentralnodesinhostpathogensinteractions AT mshahidmukhtar pipelineofintegratingtranscriptomeandinteractometoelucidatecentralnodesinhostpathogensinteractions |