RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration
Background With the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Prof...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2018-01-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/4262.pdf |
| _version_ | 1797418831754297344 |
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| author | Jing Zhang Kenneth B. Storey |
| author_facet | Jing Zhang Kenneth B. Storey |
| author_sort | Jing Zhang |
| collection | DOAJ |
| description | Background With the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA’s role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS) analysis. Methods The package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs. Results By incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow. Conclusions With RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS). More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865). |
| first_indexed | 2024-03-09T06:38:38Z |
| format | Article |
| id | doaj.art-d10f366e1bf146609fc09ec2efb8f0bb |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:38:38Z |
| publishDate | 2018-01-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-d10f366e1bf146609fc09ec2efb8f0bb2023-12-03T10:54:56ZengPeerJ Inc.PeerJ2167-83592018-01-016e426210.7717/peerj.4262RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integrationJing Zhang0Kenneth B. Storey1Schulich School of Medicine & Dentistry, University of Western Ontario, London, CanadaInstitute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, CanadaBackground With the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA’s role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS) analysis. Methods The package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs. Results By incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow. Conclusions With RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS). More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865).https://peerj.com/articles/4262.pdfLogistic regressionPathway analysisTranscriptomeGene set enrichmentMolecular biologyPost-transcriptional regulation |
| spellingShingle | Jing Zhang Kenneth B. Storey RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration PeerJ Logistic regression Pathway analysis Transcriptome Gene set enrichment Molecular biology Post-transcriptional regulation |
| title | RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration |
| title_full | RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration |
| title_fullStr | RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration |
| title_full_unstemmed | RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration |
| title_short | RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration |
| title_sort | rbiomirgs an all in one mirna gene set analysis solution featuring target mrna mapping and expression profile integration |
| topic | Logistic regression Pathway analysis Transcriptome Gene set enrichment Molecular biology Post-transcriptional regulation |
| url | https://peerj.com/articles/4262.pdf |
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