SimiRa: A tool to identify coregulation between micrornas and rna-binding proteins

Preusse M, Marr C, Saunders S, Maticzka D, Lickert H, Backofen R, Theis F (2015)

Publication Type: Journal article

Publication year: 2015

Journal

Rna Biology Landes Bioscience

Book Volume: 12

Pages Range: 998-1009

Journal Issue: 9

DOI: 10.1080/15476286.2015.1068496

Abstract

microRNAs and microRNA-independent RNA-binding proteins are 2 classes of post-transcriptional regulators that have been shown to cooperate in gene-expression regulation. We compared the genome-wide target sets of microRNAs and RBPs identified by recent CLIP-Seq technologies, finding that RBPs have distinct target sets and favor gene interaction network hubs. To identify microRNAs and RBPs with a similar functional context, we developed simiRa, a tool that compares enriched functional categories such as pathways and GO terms. We applied simiRa to the known functional cooperation between Pumilio family proteins and miR-221/222 in the regulation of tumor supressor gene p27 and show that the cooperation is reflected by similar enriched categories but not by target genes. SimiRa also predicts possible cooperation of microRNAs and RBPs beyond direct interaction on the target mRNA for the nuclear RBP TAF15. To further facilitate research into cooperation of microRNAs and RBPs, we made simiRa available as a web tool that displays the functional neighborhood and similarity of microRNAs and RBPs: http://vsicb-simira.helmholtz-muenchen.de.

Involved external institutions

Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich DE Germany (DE) Albert-Ludwigs-Universität Freiburg DE Germany (DE)

How to cite

APA:

Preusse, M., Marr, C., Saunders, S., Maticzka, D., Lickert, H., Backofen, R., & Theis, F. (2015). SimiRa: A tool to identify coregulation between micrornas and rna-binding proteins. Rna Biology, 12(9), 998-1009. https://doi.org/10.1080/15476286.2015.1068496

MLA:

Preusse, Martin, et al. "SimiRa: A tool to identify coregulation between micrornas and rna-binding proteins." Rna Biology 12.9 (2015): 998-1009.

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