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PMID: 32484539 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology.

Nucleic acids research ·Vol. 48 ·No. W1 ·2020-00-02 ·Pages W244-W251

Chang L, Zhou G, Soufan O, Xia J

Abstract

miRNet is an easy-to-use, web-based platform designed to help elucidate microRNA (miRNA) functions by integrating users' data with existing knowledge via network-based visual analytics. Since its first release in 2016, miRNet has been accessed by >20 000 researchers worldwide, with ∼100 users on a daily basis. While version 1.0 was focused primarily on miRNA-target gene interactions, it has become clear that in order to obtain a global view of miRNA functions, it is necessary to bring other important players into the context during analysis. Driven by this concept, in miRNet version 2.0, we have (i) added support for transcription factors (TFs) and single nucleotide polymorphisms (SNPs) that affect miRNAs, miRNA-binding sites or target genes, whilst also greatly increased (>5-fold) the underlying knowledgebases of miRNAs, ncRNAs and disease associations; (ii) implemented new functions to allow creation and visual exploration of multipartite networks, with enhanced support for in situ functional analysis and (iii) revamped the web interface, optimized the workflow, and introduced microservices and web application programming interface (API) to sustain high-performance, real-time data analysis. The underlying R package is also released in tandem with version 2.0 to allow more flexible data analysis for R programmers. The miRNet 2.0 website is freely available at https://www.mirnet.ca.

MeSH Terms
Computer Graphics Gene Expression Regulation Gene Regulatory Networks Humans Knowledge Bases MicroRNAs/metabolism Multiple Sclerosis/genetics,metabolism Polymorphism, Single Nucleotide Software Systems Biology Transcription Factors/metabolism
Chemicals
MicroRNAs Transcription Factors
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Chang Le
Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
Zhou Guangyan
Institute of Parasitology, McGill University, Montreal, Quebec, Canada.
Soufan Othman
Institute of Parasitology, McGill University, Montreal, Quebec, Canada.
Xia Jianguo
Department of Human Genetics, McGill University, Montreal, Quebec, Canada. | Institute of Parasitology, McGill University, Montreal, Quebec, Canada. | Department of Animal Science, McGill University, Montreal, Quebec, Canada.
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkaa467
Published
2020-00-02
Pages
W244-W251
Language
English
Region
England
NLM ID
0411011
PMCID
PMC7319552
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkaa467 PMC Full Text View journal details
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