Processed data and analysis results for 104 RBPs

DOI10.5281/zenodo.3779037Zenodo3779037MaRDI QIDQ6677481FDOQ6677481

Dataset published at Zenodo repository.

Fan Chen, Sunduz Keles

Publication date: 30 April 2020

Copyright license: Creative Commons Attribution 4.0 International

Description

This repository makes available the processed data and the resultsof our SURF paper. The paper presents the Statistical Utility for RBP Functions (SURF) for integrative analysis of RNA-seq and CLIP-seq data. The goal of SURF is to identify alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by individual RBPs and elucidate protein-RNA interactions governing these events. We appliedthe SURF pipeline to analyze 104 RBP data sets (from ENCODE) and performed downstreamanalysis. Check out the browsable results from this shinyapp! The current repository includes: meme.326.input.zip -- input of 326 MEME runs on SURF-inferred location features meme.326.output.zip -- output of 326 MEME runs on SURF-inferred location features surf_inferred_feature.gtf -- SURF-inferred location features for 52 RBPs gencode.v24.annotation.filtered.gtf -- filtered genome annotation used for ENCODE data analysis Homo_sapiens.GRCh37.71.primary_assembly.protein_coding.gtf -- genome annotation used for simulation study simulation_truth.txt -- truth parameters used for RNA-seq simulation [RBP].results.rds -- SURF output (each anR object) for 104RNA-binding proteins([RBP] theprotein name). For reproducingthe results,the source code is available at DOI:10.5281/zenodo.3779853.

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