PAR-CLIP motif analysis tool

This website provides the (linux) executable for an enrichment analysis tool for deep sequencing data generated by the newly developed PAR-CLIP¹ (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. As a first analysis step the short sequence reads are processed using the PARalyzertool that generate a high resolution set of Protein-RNA interaction sequence regions with assigned evidence of direct RNA-protein X-linking.

The motif analysis of PAR-CLIP experiments in which the RNA Binding Protein of interest is expected to interact with a single binding motif (e.g. Pum2, QKI) we apply an updated version of a recently developed method, the Evidence Ranked Motif Identification Tool² (cERMIT v1.0), which has been shown to exhibit highly competitive performance in the context of TF binding site discovery using ChIP-based high-throughput data. The executable implementing the proposed motif discovery approach (cERMIT v1.1) along with sample input and output from the analysis of Pumilio2 and Quaking and IG2FBP1 data from Hafner et al.¹ can be downloaded here. (view the readme file)

In the case of Argonaute PAR-CLIP experiment the motif analysis proceeeds by evaluation of a pre-defined set of microRNAs, based on complementary canonical seed matches in the sequence peaks inferred using the PARalyzer tool. The miRNA scoring is performed in the context of a linear regression framework, incorporating (normalized) di-nucleotide counts and an indicator variable for seed match occurrence as the peak covariates. The (linux) executable implementing the proposed enrichment analsyis approach (mEAT v1.0) along with sample input and output from the analysis of Argonaute data from Hafner et al.¹ can be downloaded here. (view the readme file)

A complete pipeline which implements the pre-processing of the PARalyzer input followed by cERMIT/mEAT analysis can be downloaded here. (view the readme file)

Note: mEAT v1.0 and cERMIT v1.1 are provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler.

[1] Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010. 141(1):p129-141

[2] Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S and Ohler U. Evidence-ranked motif identification. Genome Biology 2010. 11:R19 [website]