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:
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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
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.
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