@article{Preusse_Marr_Saunders-SimiR_tool_ident_coreg-RNABiol2015,
author = {Preusse, Martin and Marr, Carsten and Saunders, 
          Sita and Maticzka, Daniel and Lickert, Heiko and Backofen, Rolf and Theis, Fabian},
title = {Simi{R}a: A tool to identify coregulation between
         micro{RNA}s and {RNA}-binding proteins},
journal = {RNA Biology},
year = {2015},
doi = {10.1080/15476286.2015.1068496},
volume = {12},
user = {sita},
pmid = {26383775},
pages = {998-1009},
number = {9},
issn = {1547-6286},
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.}
}