miRegulome: a knowledge-base of miRNA regulomics and analysis

doi:10.1038/srep12832

. 2015 Aug 5:5:12832.

doi: 10.1038/srep12832.

miRegulome: a knowledge-base of miRNA regulomics and analysis

Affiliations

¹ Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India.
² Department of Computer Science, Virginia Commonwealth University, Richmond, VA-23284, USA.
³ 1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India [2] School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India.
⁴ 1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India [2] Laboratorio de Genetica Celular eMolecular, Departmento de Biologia Geral, Instituto de Ciencias Biologics, Universidade Federal de Minas Gerais CP 486, CEP 31270-901 Belo Horizonte, Minas Gerais, Brazil.
⁵ Laboratorio de Genetica Celular eMolecular, Departmento de Biologia Geral, Instituto de Ciencias Biologics, Universidade Federal de Minas Gerais CP 486, CEP 31270-901 Belo Horizonte, Minas Gerais, Brazil.
⁶ 1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India [2] Department of Psychiatry and McKnight Brain Institute, University of Florida, College of Medicine, Gainesville, Florida, USA.
⁷ School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India.
⁸ Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01 - Guamá, Belém, PA, Brazil.

PMID: 26243198
PMCID: PMC4525332
DOI: 10.1038/srep12832

miRegulome: a knowledge-base of miRNA regulomics and analysis

Debmalya Barh et al. Sci Rep. 2015.

. 2015 Aug 5:5:12832.

doi: 10.1038/srep12832.

Authors

Affiliations

¹ Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India.
² Department of Computer Science, Virginia Commonwealth University, Richmond, VA-23284, USA.
³ 1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India [2] School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India.
⁴ 1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India [2] Laboratorio de Genetica Celular eMolecular, Departmento de Biologia Geral, Instituto de Ciencias Biologics, Universidade Federal de Minas Gerais CP 486, CEP 31270-901 Belo Horizonte, Minas Gerais, Brazil.
⁵ Laboratorio de Genetica Celular eMolecular, Departmento de Biologia Geral, Instituto de Ciencias Biologics, Universidade Federal de Minas Gerais CP 486, CEP 31270-901 Belo Horizonte, Minas Gerais, Brazil.
⁶ 1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India [2] Department of Psychiatry and McKnight Brain Institute, University of Florida, College of Medicine, Gainesville, Florida, USA.
⁷ School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India.
⁸ Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01 - Guamá, Belém, PA, Brazil.

PMID: 26243198
PMCID: PMC4525332
DOI: 10.1038/srep12832

Abstract

miRNAs regulate post transcriptional gene expression by targeting multiple mRNAs and hence can modulate multiple signalling pathways, biological processes, and patho-physiologies. Therefore, understanding of miRNA regulatory networks is essential in order to modulate the functions of a miRNA. The focus of several existing databases is to provide information on specific aspects of miRNA regulation. However, an integrated resource on the miRNA regulome is currently not available to facilitate the exploration and understanding of miRNA regulomics. miRegulome attempts to bridge this gap. The current version of miRegulome v1.0 provides details on the entire regulatory modules of miRNAs altered in response to chemical treatments and transcription factors, based on validated data manually curated from published literature. Modules of miRegulome (upstream regulators, downstream targets, miRNA regulated pathways, functions, diseases, etc) are hyperlinked to an appropriate external resource and are displayed visually to provide a comprehensive understanding. Four analysis tools are incorporated to identify relationships among different modules based on user specified datasets. miRegulome and its tools are helpful in understanding the biology of miRNAs and will also facilitate the discovery of biomarkers and therapeutics. With added features in upcoming releases, miRegulome will be an essential resource to the scientific community.

Availability: http://bnet.egr.vcu.edu/miRegulome.

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Figures

**Figure 1. Schematic diagram of modules and their inter-relationships in a miRNA regulome.**

**Figure 2. Distribution of *miRegulome* v1.0 contents.**
(A) Overall distribution of the database contents. (B) Species specific miRNA counts.

**Figure 3. Visualization of miRNA regulome in *miRegulome* v1.0.**
The figure represents hsa-miR-200b regulome.

**Figure 4. The relationships among various modules of hsa-mir-200b suggest that this miRNA is a probable tumor suppressor.**

**Figure 5. Emerging molecular mechanism and correlation between obesity and diabetes as identified by miRegulome data.**
For details, please see the text.

See this image and copyright information in PMC

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References

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1. Hossain M. M., Salilew-Wondim D., Schellander K. & Tesfaye D. The role of microRNAs in mammalian oocytes and embryos. Anim Reprod Sci 134, 36–44 (2012). - PubMed

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[1] Filipowicz W., Bhattacharyya S. N. & Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9, 102–114 (2008). - PubMed

[2] Filipowicz W., Bhattacharyya S. N. & Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9, 102–114 (2008). - PubMed

[3] Yokoi T. & Nakajima M. Toxicological implications of modulation of gene expression by microRNAs. Toxicol Sci 123, 1–14 (2011). - PubMed

[4] Yokoi T. & Nakajima M. Toxicological implications of modulation of gene expression by microRNAs. Toxicol Sci 123, 1–14 (2011). - PubMed

[5] Gurtan A. M. & Sharp P. A. The role of miRNAs in regulating gene expression networks. J Mol Biol 425, 3582–3600 (2013). - PMC - PubMed

[6] Gurtan A. M. & Sharp P. A. The role of miRNAs in regulating gene expression networks. J Mol Biol 425, 3582–3600 (2013). - PMC - PubMed

[7] Krek A. et al. Combinatorial microRNA target predictions. Nat Genet 37, 495–500 (2005). - PubMed

[8] Krek A. et al. Combinatorial microRNA target predictions. Nat Genet 37, 495–500 (2005). - PubMed

[9] Hossain M. M., Salilew-Wondim D., Schellander K. & Tesfaye D. The role of microRNAs in mammalian oocytes and embryos. Anim Reprod Sci 134, 36–44 (2012). - PubMed

[10] Hossain M. M., Salilew-Wondim D., Schellander K. & Tesfaye D. The role of microRNAs in mammalian oocytes and embryos. Anim Reprod Sci 134, 36–44 (2012). - PubMed

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miRegulome: a knowledge-base of miRNA regulomics and analysis

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miRegulome: a knowledge-base of miRNA regulomics and analysis

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