miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis.
MicroRNAs (miRNAs) can regulate nearly all biological processes and their dysregulation is implicated in various complex diseases and pathological conditions. Recent years have seen a growing number of functional studies of miRNAs using high-throughput experimental technologies, which have produced a large amount of high-quality data regarding miRNA target genes and their interactions with small molecules, long non-coding RNAs, epigenetic modifiers, disease associations, etc These rich sets of information have enabled the creation of comprehensive networks linking miRNAs with various biologically important entities to shed light on their collective functions and regulatory mechanisms. Here, we introduce miRNet, an easy-to-use web-based tool that offers statistical, visual and network-based approaches to help researchers understand miRNAs functions and regulatory mechanisms. The key features of miRNet include: (i) a comprehensive knowledge base integrating high-quality miRNA-target interaction data from 11 databases; (ii) support for differential expression analysis of data from microarray, RNA-seq and quantitative PCR; (iii) implementation of a flexible interface for data filtering, refinement and customization during network creation; (iv) a powerful fully featured network visualization system coupled with enrichment analysis. miRNet offers a comprehensive tool suite to enable statistical analysis and functional interpretation of various data generated from current miRNA studies. miRNet is freely available at http://www.mirnet.ca.
Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada.
Yannan
Y
Fan
Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec H3G 1Y6, Canada.
Keith
K
Siklenka
Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada.
Simran K
SK
Arora
Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada.
Paula
P
Ribeiro
Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec H3G 1Y6, Canada Department of Animal Science, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada.
Sarah
S
Kimmins
Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Department of Animal Science, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada jeff.xia@mcgill.ca.
Jianguo
J
Xia
D000818:Animals; D001665:Binding Sites; D003196:Computer Graphics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D012984:Software
D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger