Abstract
The association of dysregulated microRNAs (miRNAs) and diseases has been shown in a variety of studies. Here, we review a resource denoted as PhenomiR, providing systematic and comprehensive access to such studies. It allows machine-readable access to miRNA and target relations from these studies to study the impact of miRNAs on multifactorial diseases across many samples and biological replicates. We summarize the PhenomiR data structure and its content and show how to access the database and use it in everyday miRNA profile analysis using the R language.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Friedman, R. C., Farh, K. K., Burge, C. B., and Bartel, D. P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19, 92–105.
Bishop, T. and Sham, P. (2001) Analysis of Multifactorial Diseases ELSEVIER.
Kim, Y. K., Yu, J., Han, T. S., Park, S. Y., Namkoong, B., Kim, D. H., et al. (2009) Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Nucleic Acids Res 37, 1672–81.
Mendell, J. T. (2008) miRiad roles for the miR-17-92 cluster in development and disease. Cell 133, 217–22.
Baskerville, S. and Bartel, D. P. (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241–7.
Ruepp, A., Kowarsch, A., Schmidl, D., Buggenthin, F., Brauner, B., Dunger, I., et al. (2010) PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol 11, R6.
Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., Canese, K., et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 38, D5–16.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2010) GenBank. Nucleic Acids Res 38, D46–51.
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., et al. (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25, 25–9.
Amberger, J., Bocchini, C. A., Scott, A. F., and Hamosh, A. (2009) McKusick’s Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res 37, D793–6.
Chang, A., Scheer, M., Grote, A., Schomburg, I., and Schomburg, D. (2009) BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 37, D588–92.
Griffiths-Jones, S., Saini, H. K., van, D. S., and Enright, A. J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36, D154–8.
Goh, K. I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., and Barabasi, A. L. (2007) The human disease network. Proc Natl Acad Sci USA 104, 8685–90.
Acknowledgements
This work is funded in parts by the Federal Ministry of Education and Research (BMBF), its MedSys initiative (projects LungSys and SysMBo), the Helmholtz Alliance on Systems Biology (project CoReNe), and the German Research Foundation (InKoMBio, SPP1395).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Ruepp, A., Kowarsch, A., Theis, F. (2012). PhenomiR: MicroRNAs in Human Diseases and Biological Processes. In: Fan, JB. (eds) Next-Generation MicroRNA Expression Profiling Technology. Methods in Molecular Biology, vol 822. Humana Press. https://doi.org/10.1007/978-1-61779-427-8_17
Download citation
DOI: https://doi.org/10.1007/978-1-61779-427-8_17
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-426-1
Online ISBN: 978-1-61779-427-8
eBook Packages: Springer Protocols