title: MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.
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/
authors.affiliation: Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Hong-Dong
authors.initials: HD
authors.lastname: Li
authors.affiliation: Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.affiliation: Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA gyuanfan@umich.edu.
authors.forename: Yuanfang
authors.initials: Y
authors.lastname: Guan
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D030541:Databases, Genetic; D016678:Genome; D051379:Mice; D009928:Organ Specificity; D020033:Protein Isoforms / Q000096:biosynthesis / Q000235:genetics
chemical_list: D020033:Protein Isoforms