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decode protein-lncRNA, protein-ncRNA, protein-mRNA interactions from CLIP-Seq da

lncRNA protein RNA-Binding protein interaction miRNA

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#1 zhxq09



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Posted 21 April 2014 - 03:32 AM

High-throughput sequencing of immunoprecipitated RNAs after cross-linking (CLIP-Seq, HITS-CLIP, PAR-CLIP, CLASH, iCLIP) provide powerful ways to identify biologically relevant miRNA-target and protein–RNA interactions.


related RNA binding protein-lncRNA, protein-mRNA, miRNA-lncRNA resources:

(1) starBase had integrated 111 CLIP-Seq (HITS-CLIP, PAR-CLIP, CLASH, iCLIP) datasets to decipher interactions between RNA-Binding Proteins (RBPs) and RNAs, such as protein-lncRNAprotein-sncRNAprotein-mRNA andprotein-pseudogene interactions.

includes RNA-Binding Proteins:
related with epigenetics: PRC2(EZH2)
related with brain: TDP-43, FMRP, Nova
related with splicing and transcription: PTB, HnRNPC
others: HuR, PUM2, QKI, IGF2BP1-3, FUS, DGCR8, TNRC6, LIN28, UPF1 etc...


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