NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 03 2023
01 03 2023
Historique:
received:
21
10
2022
revised:
16
01
2023
accepted:
17
02
2023
pubmed:
8
3
2023
medline:
22
3
2023
entrez:
7
3
2023
Statut:
ppublish
Résumé
The investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes that are active or modulated in a specific experimental context. The Network Data Exchange Integrated Query (NDEx IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The NDEx IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. NDEx IQuery's integration with MSigDB and cBioPortal now provides pathway analysis in the context of these two resources. NDEx IQuery is available at https://www.ndexbio.org/iquery and is implemented in Javascript and Java.
Identifiants
pubmed: 36882166
pii: 7070501
doi: 10.1093/bioinformatics/btad118
pmc: PMC10023220
pii:
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NCI NIH HHS
ID : U54 CA274502
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG012107
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA184427
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103504
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA269436
Pays : United States
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
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