SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
starBase: deciphering miRNA-target interactions from CLIP-Seq and Degradome-Seq data rnaNGS RNA Sequencing 7 02-14-2013 08:38 PM
NovoPackage, Python tools for analysis of CLIP, CRAC or RNA seq data g_ronimo Bioinformatics 16 12-23-2011 04:23 AM
starBase: explore microRNA–mRNA interaction maps from CLIP-Seq and Degradome-Seq data yjhua2110 Literature Watch 1 02-02-2011 08:50 AM
ChIP-Seq: Integrative analysis of genomic, functional and protein interaction data pr Newsbot! Literature Watch 0 11-27-2010 03:02 AM
Annotating mRNA-Seq maps/alignments atg...tga Bioinformatics 0 11-05-2009 02:59 PM

Reply
 
Thread Tools
Old 10-30-2010, 03:01 AM   #1
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 67
Default starBase: explore microRNA–mRNA interaction maps from CLIP-Seq and Degradome-Seq data

Dear All,

Here, we introduce a public platform, starBase (sRNA target Base), for exploring microRNA-target interaction maps from Argonaute (Ago) CLIP-Seq (HITS-CLIP,PAR-CLIP) and degradome sequencing (Degradome-Seq, PARE) data.

CLIP-Seq (HITS-CLIP,PAR-CLIP) and Degradome-Seq (PARE) are the newest high-throughput technology for the transcriptome-wide identification of miRNA target sites in animals and plants. Currently, starBase contains high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms: human, mouse, C.elegans, Arabidopsis thaliana, Rice, Grapevine.

the distinctive features in our starBase are as follows:

(i) our improved deepView Genome Browser was developed to provide an integrated view of multidimensional data, including predicted targets (targetScan (V5.1), miRanda, picTar, RNA22, PITA and CleaveLand), known targets, known ncRNAs, genes, clusters....

(ii) Target site intersections : Search for intersections among targets predicted by different target prediction programs[targetScan, miRanda, picTar, RNA22 and PITA].

(iii)MiRNA-target interactions: animal miRNA-target and plant miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively.

(iv) Two web servers, ClipSearch and DegradomeSearch, were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data.

Please visit http://starbase.sysu.edu.cn/ or read our starBase paper (Nucleic Acids Res. 2011;39: D202-D209. doi: 10.1093/nar/gkq1056, First published online: October 30, 2010) for details.

This is the first version of starBase database. We look forward to your feedback.

Thanks!
JianHua

Last edited by yjhua2110; 03-04-2011 at 11:24 PM.
yjhua2110 is offline   Reply With Quote
Old 11-05-2010, 12:56 AM   #2
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 67
Default deepView genome browser to browse microRNA targets

You can use our improved deepView Genome browser to browse and simultaneously compare the microRNA targets predicted by TargetScan (V5.1), PicTar, miRanda, PITA(top), RNA22 and CleaveLand (for plant) target prediction softwares.


Last edited by yjhua2110; 11-18-2010 at 05:15 AM.
yjhua2110 is offline   Reply With Quote
Old 11-10-2010, 08:10 PM   #3
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 67
Default integrating mirSVR microRNA targets into starBase

mirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score (Betel et al. Genome Biology 2010, 11:R90) . mirSVR was developed by Leslie's group at Memorial Sloan-Kettering Cancer Center.

We have integrated microRNA targets predicted by mirSVR into our starBase. You can browse the mirSVR microRNA targets using our deepView Genome Browser.
yjhua2110 is offline   Reply With Quote
Old 11-18-2010, 05:26 AM   #4
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 67
Default integrate Binding site dataset for other RNA-binding proteins (RBPs) into starBase

Binding sites (clusters) for other RNA-binding proteins (RBPs)(PUM2, QKI, IGF2BP1, IGF2BP2 and IGF2BP3) obtained from Tuschl lab (Hafner et al. Cell. 2010 Apr 2;141(1):129-41.) were added in our starBase and displayed in our deepView genome browser.

Last edited by yjhua2110; 11-18-2010 at 05:28 AM.
yjhua2110 is offline   Reply With Quote
Old 04-19-2011, 12:50 AM   #5
rnaNGS
Member
 
Location: China

Join Date: Dec 2009
Posts: 43
Default

CLIP-Seq clusters (peaks) for polypyrimidine tract-binding protein (PTB) (Xue et al. Mol. Cell 2009;36:996-1006.) were added in our starBase and displayed in our deepView genome browser.
rnaNGS is offline   Reply With Quote
Old 05-09-2011, 06:33 AM   #6
rnaNGS
Member
 
Location: China

Join Date: Dec 2009
Posts: 43
Default Mouse embryonic stem cells(ESC) Ago2 CLIP-Seq clusters

Mouse embryonic stem cells(ESC) Ago2 CLIP-Seq clusters (Leung et al. Nat Struct Mol Biol. 2011 Feb;18(2):237-44.) obtained from Sharp lab were added in our starBase and displayed in our deepView genome browser.
rnaNGS is offline   Reply With Quote
Old 05-19-2011, 08:06 AM   #7
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 67
Default Human and Mouse TDP-43 CLIP-Seq(iCLIP) clusters

Binding sites (clusters) for Human and Mouse TDP-43 (Tollervey et al. Nat Neurosci. 2011 Apr;14(4):452-8; Polymenidou et al. Nat Neurosci. 2011 Apr;14(4):459-68.) obtained from from Ule and Yeo labs were added in our starBase.
yjhua2110 is offline   Reply With Quote
Old 05-25-2011, 08:48 PM   #8
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 67
Default the release of starBase v2.0, miRNA-target and protein-RNA interaction maps

We are pleased to announce the release of starBase v2.0. In this release, we provided protein-RNA interaction maps from other RNA Binding Proteins, including FOX2, IGF2BP1, IGF2BP2, IGF2BP3, PTB, PUM2, QKI, TDP-43, TNRC6, AGOs/ALG1 and Nova. In addition, we provided many filter steps to guide user to select high-confidence microRNA targets, such as microRNA expression abundance, biology complex, etc.
yjhua2110 is offline   Reply With Quote
Old 09-27-2011, 08:45 AM   #9
rnaNGS
Member
 
Location: China

Join Date: Dec 2009
Posts: 43
Default microRNA regulatory networks

starBase provides two new tools, miRPathway and miRGO, to explore microRNA regulatory networks by combining Gene Ontology (GO) categories, KEGG biological pathways and high-confidence microRNA targets overlapping with CLIP-Seq data.
rnaNGS 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 06:54 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO