RNA-RNA interactions (RRIs) in RISE are from high-throughput sequencing-based experiments and other public available (primary) databases and datasets. The following table gives the detailed source information. Briefly, RISE curated RRIs from 3 types of sources----transcriptome-wide studies, targeted studies, and other databases/datasets. Among them, transcriptome-wide studies use PARIS, MARIOS, SPLASH, LIGR-seq technologies to discover RRIs, and targeted studies use RIA-seq, RAP-RNA, CLASH. The “other databases/datasets” include RRIs from the NPInter v3.0, RAID v2.0, RAIN databases, and the Lai D, et al. 2016 datasets（published in PMID: 26673718). Currently, RRIs in RISE come from 5 species --human, mouse, yeast, E.coli, S.enteria, or 10 different cell lines.
| 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 | RA | 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 | 7,260 | |
| Yeast | BY4741 (miRNAs) | 253 | 47 | ||
| From other databases/datasets | 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 |
mESCa: This experiment used in MARIO detects RRIs directly connected by one protein.
mESCb: This experiment used in MARIO detects RRIs connected by multiple proteins.
The following pie plots show the number of RNA-RNA interactions in RISE, per species, cell line and method/source.
The following circos plots show the number of RNA-RNA interactions (RRIs) within/between different types of RNAs, including mRNAs, lncRNAs, miRNAs, rRNAs, snoRNAs, snRNAs, tRNAs, non-canonical RNAs, and others( Transposable element, pseudogene).
As a unique feature, the majority of RRIs in RISE involve mRNAs and lncRNAs.