Table 1. Overview of data collected in the RISE database.
| Category | Method/Resource | Species | Cell line | Number of interactions | Number of involved genes |
|---|---|---|---|---|---|
| Transcriptome-wide studies | PARIS | Human | HEK293T | 25 824 | 16 192 |
| Human | Hela (high RNase) | 25 552 | 19 335 | ||
| Human | Hela (low RNase) | 20 330 | 17 009 | ||
| Mouse | mESC | 29 514 | 12 625 | ||
| MARIO | Mouse | MEF | 7 167 | 2 936 | |
| Mouse | mESCa | 99 290 | 15 309 | ||
| Mouse | mESCb | 37 441 | 9 715 | ||
| SPLASH | Human | hESC | 3 345 | 971 | |
| Human | HeLa | 5 799 | 1 649 | ||
| Human | LCL | 4 213 | 429 | ||
| Human | hESC (RA treated) | 1 770 | 671 | ||
| LIGR-seq | Human | HEK293T | 641 | 749 | |
| Targeted studies | RIA-seq | Human | Keratinocytes (TINCR) | 3 609 | 1 815 |
| RAP-RNA | Mouse | mESC (Malat1) | 495 | 489 | |
| Mouse | mESC (U1 snRNA) | 12 278 | 8 635 | ||
| CLASH | Human | HEK293 (miRNAs) | 18 508 | 7260 | |
| Yeast | BY4741 (miRNAs) | 253 | 47 | ||
| From other databases/dataset | NPInter v3.0 | Human | − | 3 691 | 2 525 |
| Mouse | − | 52 | 83 | ||
| RAID v2.0 | Human | − | 22 521 | 6 262 | |
| Mouse | − | 3 440 | 2 130 | ||
| RAIN | Human | − | 2 881 | 1 189 | |
| Mouse | − | 36 | 31 | ||
| PMID 26673718 | E. coli | − | 64 | 68 | |
| S. enterica | − | 45 | 49 | ||
| Yeast | − | 52 | 45 | ||
| Total | − | − | − | 328 811 | 56 295 |
aThis experiment uses UV-crosslinking to detect RRIs mediated by one protein.
bThis experiment uses chemical crosslinking to detect RRIs mediated by multiple proteins.