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PARma: identification of microRNA target sites in AGO-PAR-CLIP data |
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| Authors: | Florian Erhard Lars D?lken Lukasz Jaskiewicz Ralf Zimmer |
| Institution: | 1.Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany;2.Department of Medicine, University of Cambridge, Box 157, Level 5, Addenbrooke''s Hospital, Hills Road, CB2 0QQ Cambridge, UK;3.Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstr. 50/70, CH-4056, Basel, Switzerland |
| Abstract: | PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma |
| Keywords: | PAR-CLIP microRNA generative model EM algorithm |