All the RNA-RNA interaction (RRI) data in the RISE database can be downloaded.
The RRIs are organized into datasets by different species and technologies.
| Species | Transcriptome-wide studiesa | Targeted studiesb | From other databases/datasetsc | Whole RNA-RNA interactome |
|---|---|---|---|---|
| human | 87,474 (2.9 MB) | 22,117 (528 KB) | 29,093 (576 KB) | 138,684 (4 MB) |
| mouse | 173,412 (6.6 MB) | 12,773 (288 KB) | 3,528 (72 KB) | 189,713 (6.9 MB) |
| yeast | 0 (0 KB) | 253 (4 KB) | 52 (4 KB) | 305 (8 KB) | all species | 260,886 (9.5 MB) | 35,143 (820 KB) | 32,782 (652 KB) | 328,811 (11 MB) |
a:Transcriptome-wide studies: PARIS, MARIO, SPLASH, LIGR-seq
b:Targeted studies: RIA-seq, RAP-RNA, CLASH
c:From other databases/datasets: NPInter v3.0, RAID v2.0, RAIN v1.0, Lai D, et al. datasets published in PMID: 26673718 in Nucleic Acids Res (2016)
Downloads file format
The RRI data are in the BEDPE file format, defined in BEDTOOLS. Each entry denote an RRI(RNA-RNA Interaction).
The following are the details of each column. Here RNA1 and RNA2 are the two interacting RNAs :
1. chr1: The name of the chromosome of the first RNA.
2. start1: The zero-based starting position of the interacting region on chr1.
3. end1: The one-based ending position of interacting region on chr1.
4. chr2: The name of the chromosome of the second RNA.
5. start2: The zero-based starting position of the interacting region on chr2.
6. end2: The one-based ending position of the interacting region on chr2.
7. rise_id: The interaction entry ID in RISE.
8. score: All " . " here (just adapt to file format).
9. strand1: Defines the strand for the RNA1. Either '+'' or '-'. Note: if some entry source provides no strand information, we use " . " instead.
10. strand2: Defines the strand for the RNA2. Either '+' or '-'. Note: if some entry source provides no strand information, we use " . " instead.
11. gene_id1: Ensembl gene id of RNA1. Note: if there is no available Ensembl gene id, use " . " instead.
12. gene_name1.
13. gene_id2: Ensembl gene id of RNA2. Note: if there is no available Ensembl gene id, use " . " instead.
14. gene_name2.
15. gene_type1: Gene type of RNA1.
16. gene_type2: Gene type of RNA2.
17. genomic_context1: Genomic context of RNA1 interaction region. Note: if there is no interacting region information, use " . " instead.
18. genomic_context2: Genomic context of RNA2 interaction region. Note: if there is no interacting region information, use " . " instead.
19. method: RNA interaction detected method.
10. species.
21. cell line: Cell line of the detected interaction. Note: for interaction from other databases, there is no cell line information, use " . " instead.
22. pubmed_id: Pubmed id of the reference paper where the interaction from.