Downloads

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.