Tool: Deciphering LncRNA-Target, NcRNA-Target, Pseudogene-Target and mRNA-Target Interactions from RNA Interactome Sequencing Data
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gravatar for lsp03yjh
7 weeks ago by
lsp03yjh720
China
lsp03yjh720 wrote:

We constructs a global-scale landscape of RNA-RNA interactions involving various classes of ncRNAs (lncRNAs, snoRNAs, tRNAs, snRNAs, pseudogenes and miRNAs) and mRNAs by re-analyzing high-throughput RNA interactome data from SPLASH, MARIO, PARIS and LIGR-seq methods. We using stringent parameters to filter all RNA-RNA interactions and identified ~0.1 million lncRNA-RNA interactions, ~1.2 million mRNA-RNA interactions and ~0.4 million small ncRNAs(sncRNAs)-RNA interactions, such as snoRNA-target, snRNA-target and miRNA-target interactions.

We also provides minimum free energy (MFE), smith-waterman alignment score, pairwise alignments and experimental number to allow user to filter these RNA-RNA interactions. A huge number of novel RNA-RNA interactions highlight the complexity of RNA interactomes and serve as important resources for elucidating the regulatory network of various ncRNAs and understanding the biological functions of RNA organization.

All RNA interactomes is freely available at following websites:

small ncRNA-target interactions: http://starbase.sysu.edu.cn/rnaRNA.php?source=sncRNA

lncRNA-target interactions: http://starbase.sysu.edu.cn/rnaRNA.php?source=lncRNA

mRNA-target interactions: http://starbase.sysu.edu.cn/rnaRNA.php?source=mRNA

pseudogene-target interactions: http://starbase.sysu.edu.cn/rnaRNA.php?source=pseudogene

RNA-RNA interaction example: enter image description here

ADD COMMENTlink modified 5 weeks ago • written 7 weeks ago by lsp03yjh720

Thank you for your hard work. Looks pretty neat. However, I find some details are missing such as biological source, high-throughput methods and transcript regions. See http://rise.life.tsinghua.edu.cn/downloads.html

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by lcscs1234510

Thanks for your appraisal of our platform. In fact, we provide more details in our website. You can click the web-links to get detail information such as biological source, high-throughput methods, transcript regions, read numbers. In addition, we provide the aligned regions (base-pairs), minimum free energy and align score generated by RNAfold and Smith-Waterman algorithm. These information might help researchers to select the important RNA-RNA interactions related with biological functions. We also provide Web API (http://starbase.sysu.edu.cn/tutorialAPI.php) to access all regulatory data stored within the server.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by lsp03yjh720

Thank you! I've missed out the web links that have the experimental accession numbers. However, the script below could not retrieve the accession numbers. Could you kindly show me how to do it?

curl 'http://starbase.sysu.edu.cn/api/RNARNA/?assembly=hg19&geneType=mRNA&RNA=all&interNum=1&expNum=1&cellType=all' > starBaseV3_hg19_RNA-RNA.txt

ADD REPLYlink modified 2 days ago • written 2 days ago by lcscs1234510
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