Guan Lab

Department of Computational Medicine & Bioinformatics
Sun, 07/19/2015 - 23:12 -- gyuanfan
TitleMIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.
Publication TypeJournal Article
Year of Publication2015
AuthorsLi H-D, Omenn GS, Guan Y
JournalDatabase (Oxford)
Volume2015
Paginationbav045
Date Published2015
ISSN1758-0463
Abstract

Products of multiexon genes, especially in higher organisms, are a mixture of isoforms with different or even opposing functions, and therefore need to be treated separately. However, most studies and available resources such as Gene Ontology provide only gene-level function annotations, and therefore lose the differential information at the isoform level. Here we report MIsoMine, a high-resolution portal to multiple levels of functional information of alternatively spliced isoforms in the mouse. This data portal provides tissue-specific expression patterns and co-expression networks, along with such previously published functional genomic data as protein domains, predicted isoform-level functions and functional relationships. The core utility of MIsoMine is allowing users to explore a preprocessed, quality-controlled set of RNA-seq data encompassing diverse tissues and cell lineages. Tissue-specific co-expression networks were established, allowing a 2D ranking of isoforms and tissues by co-expression patterns. The results of the multiple isoforms of the same gene are presented in parallel to facilitate direct comparison, with cross-talking to prioritized functions at the isoform level. MIsoMine provides the first isoform-level resolution effort at genome-scale. We envision that this data portal will be a valuable resource for exploring functional genomic data, and will complement the existing functionalities of the mouse genome informatics database and the gene expression database for the laboratory mouse. Database URL: http://guanlab.ccmb.med.umich.edu/misomine/

DOI10.1093/database/bav045
Alternate JournalDatabase (Oxford)
PubMed ID25953081
PubMed Central IDPMC4423410
Grant List1R21NS082212-01 / NS / NINDS NIH HHS / United States
U54ES017885 / ES / NIEHS NIH HHS / United States