Dataset Information

NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs.

ABSTRACT: MicroRNAs are a class of small RNAs known to regulate gene expression at the transcript level, the protein level, or both. Since microRNA binding is sequence-based but possibly structure-specific, work in this area has resulted in multiple databases storing predicted microRNA:target relationships computed using diverse algorithms. We integrate prediction databases, compare predictions to in vitro data, and use cross-database predictions to model the microRNA:transcript interactome--referred to as the micronome--to study microRNA involvement in well-known signalling pathways as well as associations with disease. We make this data freely available with a flexible user interface as our microRNA Data Integration Portal--mirDIP (http://ophid.utoronto.ca/mirDIP).mirDIP integrates prediction databases to elucidate accurate microRNA:target relationships. Using NAViGaTOR to produce interaction networks implicating microRNAs in literature-based, KEGG-based and Reactome-based pathways, we find these signalling pathway networks have significantly more microRNA involvement compared to chance (p<0.05), suggesting microRNAs co-target many genes in a given pathway. Further examination of the micronome shows two distinct classes of microRNAs; universe microRNAs, which are involved in many signalling pathways; and intra-pathway microRNAs, which target multiple genes within one signalling pathway. We find universe microRNAs to have more targets (p<0.0001), to be more studied (p<0.0002), and to have higher degree in the KEGG cancer pathway (p<0.0001), compared to intra-pathway microRNAs.Our pathway-based analysis of mirDIP data suggests microRNAs are involved in intra-pathway signalling. We identify two distinct classes of microRNAs, suggesting a hierarchical organization of microRNAs co-targeting genes both within and between pathways, and implying differential involvement of universe and intra-pathway microRNAs at the disease level.

SUBMITTER: Shirdel EA

PROVIDER: S-EPMC3045450 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

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NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs.

Shirdel Elize A EA Xie Wing W Mak Tak W TW Jurisica Igor I

PloS one 20110225 2

<h4>Background</h4>MicroRNAs are a class of small RNAs known to regulate gene expression at the transcript level, the protein level, or both. Since microRNA binding is sequence-based but possibly structure-specific, work in this area has resulted in multiple databases storing predicted microRNA:target relationships computed using diverse algorithms. We integrate prediction databases, compare predictions to in vitro data, and use cross-database predictions to model the microRNA:transcript interac ...[more]

PMID: 21364759

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Dataset Information

NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs.

Publications

NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs.

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