Tool:Discovering protein-lncRNA interactions from large-scale CLIP-Seq and TCGA Cancer datasets
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6.9 years ago
lsp03yjh ▴ 810

We had released RBP-lncRNA Platform to decode interaction between lncRNAs and RNA-binding proteins (RBPs) by mining 111 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH, eCLIP, irCLIP) datasets.

RBP-lncRNA platform provides the following Analysis Services:

1. We provideinteractive web-page to display the 22,735 RBP–lncRNA regulatory relationships identified from 117 CLIP-Seq datasets generated by 50 independent studies.

2. We also revealed the expression correlation of RBP-lncRNA interaction networks by mining expression profiles of over 6000 normal and tumor samples from 14 cancer types. 

3. We found that one single lncRNA will generally be bound and regulated by one or multiple RBPs, the combination of which may coordinately regulate gene expression. 

4. We discovered hundreds of disease-related single nucleotide polymorphisms (SNP) resided in the RBP binding sites of lncRNAs.

The paper has been published in Front Bioeng Biotechnol. 2015;2:88.

RBP-lncRNA Interaction web site: http://starbase.sysu.edu.cn/rbpClipRNA.php?source=lncRNA

RBP–lncRNA interactions are supported by co-expression analysis in 14 types of cancers.

 

RNA-Seq lncRNA CLIP-Seq RBP cancer Tool • 3.8k views
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