Genomics Inform.  2019 Mar;17(1):e10. 10.5808/GI.2019.17.1.e10.

HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes

• Kim Y
• Park T

• KMID: 2447800
• DOI: http://doi.org/10.5808/GI.2019.17.1.e10

Abstract

To identify miRNA-mRNA interaction pairs associated with binary phenotypes, we propose a hierarchical structural component model for miRNA-mRNA integration (HisCoM-mimi). Information on known mRNA targets provided by TargetScan is used to perform HisCoM-mimi. However, multiple databases can be used to find miRNA-mRNA signatures with known biological information through different algorithms. To take these additional databases into account, we present our advanced application software for HisCoM-mimi for binary phenotypes. The proposed HisCoM-mimi supports both TargetScan and miRTarBase, which provides manually-verified information initially gathered by text-mining the literature. By integrating information from miRTarBase into HisCoM-mimi, a broad range of target information derived from the research literature can be analyzed. Another improvement of the new HisCoM-mimi approach is the inclusion of updated algorithms to provide the lasso and elastic-net penalties for users who want to fit a model with a smaller number of selected miRNAs and mRNAs. We expect that our HisCoM-mimi software will make advanced methods accessible to researchers who want to identify miRNA-mRNA interaction pairs related with binary phenotypes.

Keyword

integration analysis; miRNA; miRNA database; mRNA

MeSH Terms

MicroRNAs
Phenotype*
RNA, Messenger
MicroRNAs
RNA, Messenger