SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
decode protein-lncRNA, protein-ncRNA, protein-mRNA interactions from CLIP-Seq data yjhua2110 RNA Sequencing 9 06-04-2015 12:12 AM
starBase v2.0: decoding miRNA-ncRNA, miRNA-ceRNA and protein-RNA interactions rnaNGS RNA Sequencing 0 09-26-2013 03:18 AM
starBase: deciphering miRNA-target interactions from CLIP-Seq and Degradome-Seq data rnaNGS RNA Sequencing 7 02-14-2013 08:38 PM

Reply
 
Thread Tools
Old 12-11-2013, 11:55 PM   #1
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 67
Default pubMed: starBase v2.0: decoding miRNA-ceRNA, miRNA-lncRNA, protein-RNA interactions

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.

Nucleic Acids Res. 2013 Dec 1.

Authors: Li JH, Liu S, Zhou H, Qu LH, Yang JH.

Abstract
Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs) (e.g. lncRNAs, pseudogenes and circRNAs) and competing endogenous RNAs (ceRNAs) have been implicated in cell-fate determination and in various human diseases, surprisingly little is known about the regulatory interaction networks among the multiple classes of RNAs. In this study, we developed starBase v2.0 (http://starbase.sysu.edu.cn/) to systematically identify the RNA-RNA and protein-RNA interaction networks from 108 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH) data sets generated by 37 independent studies. By analyzing millions of RNA-binding protein binding sites, we identified ∼9000 miRNA-circRNA, 16 000 miRNA-pseudogene and 285 000 protein-RNA regulatory relationships. Moreover, starBase v2.0 has been updated to provide the most comprehensive CLIP-Seq experimentally supported miRNA-mRNA and miRNA-lncRNA interaction networks to date. We identified ∼10 000 ceRNA pairs from CLIP-supported miRNA target sites. By combining 13 functional genomic annotations, we developed miRFunction and ceRNAFunction web servers to predict the function of miRNAs and other ncRNAs from the miRNA-mediated regulatory networks. Finally, we developed interactive web implementations to provide visualization, analysis and downloading of the aforementioned large-scale data sets. This study will greatly expand our understanding of ncRNA functions and their coordinated regulatory networks.

PMID: 24297251 [PubMed]

http://www.ncbi.nlm.nih.gov/pubmed/24297251
yjhua2110 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:16 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO