MicroRNA

Post-analysis categorization
- Literature search
Post-survey categorization
- Features validated in most cases
- Features not validated
Simple lists
Preliminary lists

Tool name

StarBase

URL

http://starbase.sysu.edu.cn/

Important features

Web based resource to study microRNA- mRNA interaction network data obtained from Argonaute CLIP-Sequencing and Degradome-Sequencing experiments.

Citations

Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res. 2011 Jan;39(Database issue):D202-9. Epub 2010 Oct 30. PubMed PMID: 21037263

Year of publication

2011

Rank by usage frequency

Comments

Function

EXPERIMENTAL data analysis, http://starbase.sysu.edu.cn/, Web based resource to study microRNA- mRNA interaction network data obtained from Argonaute CLIP-Sequencing and Degradome-Sequencing experiments. , Yang JH- Li JH- Shao P- Zhou H- Chen YQ- Qu LH. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res. 2011 Jan;39(Database issue):D202-9. Epub 2010 Oct 30. PubMed PMID: 21037263, 2011, 98, Online/ downloadable , I. SPECIES SUPPORTED INCLUDE: mammal- worm- plant II. QUERY OR INPUT DATA: 1. Input the genomic region- gene name or browse the predicted microRNA targets overlapping with CLIP-Sequencing and degradome sequencing data or TargetScan (V5.1)- PicTar- miRanda- PITA(top)- RNA22 and CleaveLand (for plant). 2. Select RNA-binding protein to search for RNA -protein interactions from CLIP-Seq data 3. Select single or multiple microRNAs for KEGG or GO analysis for miRNA target genes overlapping with CLIP-Seq data 4. Select clade- genome and database to browse CLIP-Seq and Degradome-Seq clusters generated by StarBase. III. OUTPUT DATA: depending on the chosen type of analysis the output could be related to details on microRNA target interactions overlapping with CLIP sequencing data- degradome data or selected algorithms- RNA binding proteins- results of pathway or GO analysis- CLIP seq and degradome seq clusters (peak cluster). Results are displayed in the genome browser or tabular format.