The download data includes the whole transcriptome-wide RNA structural information in different species and cell lines, the pre-calculated RBP binding sites of all 168 RBPs in whole transcriptome in K562 cells and HepG2 cells by PrismNet models with sequence information or integrated sequence and structural information in the matched cells and the experimental binding sites from eCLIP. Also, we provide a link to visualized the structure and RBP binding sites.

RNA structural information

The details of each column: transcript ID, transcript length, RPKM (or *), SHAPE score of each nucleotide (0-1, and NULL)

Pre-calculated RBP binding sites

The details of each column: chromosome, start sites, stop sites, protein name, binding probability (affinity strength for eCLIP data), strand.

RBP Footprint Challenge @ RNA Society 2021 Meeting

We predicted RBP binding sites depending on RNA structural information but excluding the sequence information (we called PrismNet-structure). Here is the trained model and predicted binding sites of SND1 protein which is a canonical double-stranded RNA binding protein.

Visualize RNA structure and RBP binding sites

You can visualize the RNA structure and RBP binding sites in the following websites:

http://prismnet.zhanglab.net/