HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes
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...
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| Language: | English |
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BioMed Central
2019-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2019-17-1-e10.pdf |
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| author | Yongkang Kim Taesung Park |
| author_facet | Yongkang Kim Taesung Park |
| author_sort | Yongkang Kim |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-299d7d51013a44f5ae6f893d9c18b1fa |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2019-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-299d7d51013a44f5ae6f893d9c18b1fa2025-02-02T13:29:27ZengBioMed CentralGenomics & Informatics2234-07422019-03-0117110.5808/GI.2019.17.1.e10553HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypesYongkang Kim0Taesung Park1 Department of Statistics, Seoul National University, Seoul 08826, Korea Department of Statistics, Seoul National University, Seoul 08826, KoreaTo 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.http://genominfo.org/upload/pdf/gi-2019-17-1-e10.pdfintegration analysismiRNAmiRNA databasemRNA |
| spellingShingle | Yongkang Kim Taesung Park HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes Genomics & Informatics integration analysis miRNA miRNA database mRNA |
| title | HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes |
| title_full | HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes |
| title_fullStr | HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes |
| title_full_unstemmed | HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes |
| title_short | HisCoM-mimi: software for hierarchical structural component analysis for miRNA-mRNA integration model for binary phenotypes |
| title_sort | hiscom mimi software for hierarchical structural component analysis for mirna mrna integration model for binary phenotypes |
| topic | integration analysis miRNA miRNA database mRNA |
| url | http://genominfo.org/upload/pdf/gi-2019-17-1-e10.pdf |
| work_keys_str_mv | AT yongkangkim hiscommimisoftwareforhierarchicalstructuralcomponentanalysisformirnamrnaintegrationmodelforbinaryphenotypes AT taesungpark hiscommimisoftwareforhierarchicalstructuralcomponentanalysisformirnamrnaintegrationmodelforbinaryphenotypes |