Table 1 RBP-centric features employed to uncover the predictor variables likely to explain the variations in the extent of conservation of binding sites for RBPs
From: Human protein-RNA interaction network is highly stable across mammals
Variable | Name of Feature | Description |
|---|---|---|
Response | Median extent of conservation of binding sites of RBPs across species. | For each RBP, the median extent of conservation of binding sites was calculated by computing the median of percentage of species each binding site was conserved in. |
Predictors | Tissue Specificity Index (Ï„) | TSI for each RBP was found using the TSI formula as described in a previous study [59] using protein level expression data of RBPs from Human Proteome Map [60]. |
| Â | Number of binding sites | For each RBP, the total number of binding sites from the BED file that mapped to a block in the MAF file was considered. |
| Â | Length of transcript | The length of transcript for each RBP was obtained from Ensembl Biomart [61]. Average of lengths were considered if multiple transcripts were present for an RBP. |
| Â | Number of protein-protein interactions | For each RBP, the number of interacting partners was calculated with data obtained from BioGRID [62]. |
| Â | Median protein level expression of RBPs across tissues | Protein level expression across 17 adult tissues was calculated for each RBP from protein level expression matrix available on Human Proteome Map [60]. |
|  | Median transcript level expression of RBPs across tissues | Transcript level expression of RBPs across 16 tissues was calculated using Human BodyMap 2.0 data from Ensembl [39]. |
| Â | Number of RNA-binding domains | Number of RNA binding domains for each RBP was obtained from a previous study on human RBPs [14]. |
| Â | Number of Paralogs | The number of paralogs for each RBP was obtained from Ensembl [39]. |
| Â | Number of sub-cellular compartments | For each RBP, the number of sub-cellular compartments that it is present in was found from UniProt [63]. |
| Â | Conservation of RBPs | The number of species that each RBP was conserved in was obtained from a previous study [14]. |
| Â | Number of RBP-RBP interactions | For each RBP, the number of interacting RBPs was computed using data from BioGRID [62]. |