Data sources

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.

Basic Statistics

The following pie plots show the number of RNA-RNA interactions in RISE,  per species, cell line and method/source.

RRIs in different species
RRIs in different cell lines
RRIs from different sources
Interactions between different types of RNAs

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.