RAIN: RNA–protein Association and Interaction Networks

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Interaction flatfiles

Flatfiles containing microRNA-target, ncRNA-protein and ncRNA-ncRNA interactions available in RAIN. All interactions are benchmarked and assigned a confidence score based on their agreement with a gold standard set of 152 miRNA-mRNA interactions (v1.croft.tsv.gz) supplemented with 630 experimentally supported high-confidence interactions to form the final gold standard (v1.extended.gold.standard.tsv.gz).

 Homo sapiens Mus musculus Rattus norvegicus Saccharomyces cerevisiae ALL ORGANISMS
Curated [1]   here   not available  not available  not available  here
Experiments [2]  here  here here  here  here
Text mining [3]  here  here  here  here  here
Predictions [4]  here   here  here  not available  here

[1] Curated knowledge on associations covering miRNA, rRNA, tRNA, SRP RNA, Vault RNA, YRNA and Telomerase RNA in Homo sapiens
[2] Experimentally supported microRNA-target, ncRNA-protein and ncRNA-ncRNA interactions
[3] microRNA-target, ncRNA-protein and ncRNA-ncRNA cooccurrences from text mining. These interactions are updated weekly, archived text mining interactions (up to two years): here
[4] Predicted miRNA-target interactions

The flatfiles have the following format (columns separated by tab) and do not contain a column header:
Organism (NCBI taxonomy id.)   ID1   ID2  Directed  Evidence  Score  Source  URL  Comment
9606  ENSPxyz  tRNAxyz   0   databases  0.900  Rfam  http://...  example1
9606  hsa-miR-xyz  ENSPxyz  1  experiments  0.700  TarBase  http://...   example2
...  ...  ...  ...  ...  ...  ...  ...  ...

NB: The search interface only returns interactions with a confidence score greater than 0.15 while the flatfiles on this page contain all interactions, irrespective of their confidence score.

Combined confidence scores

The following files contained combined confidence scores:
Homo sapiens Mus musculus Rattus norvegicus Saccharomyces cerevisiae ALL ORGANISMS
here   here  here  here  here
The files have the following format (columns separated by tab) and do not contain a column header:
Organism (NCBI taxonomy id.)   ID1   ID2  Evidence   Combined score
9606  hsa-miR-xyz  ENSPxyz   prediction   0.111
9606  hsa-miR-xyz  ENSPxyz  experimental;textmining;  0.394
...  ...  ...  ...  ...

ncRNA alias

ncRNA aliases used in RAIN: v1.rna.aliases.complete.txt.gz

The alias file has the following format (columns separated by tab) and contains a column header:
Organism (NCBI taxonomy id.)   RAIN ID Alias   Source
9606   HOTAIR  HGNC:33510  HGNC
10090  mmu-miR-708-3p   mmu-miR-708*   miRBase
...  ...  ...  ...

Interaction and alias file on FigShare

Copies of all files linked above for RAIN v1 are available on FigShare.

Source code on GitHub

Source code for our pipeline generating the RAIN interaction files is available on GitHub.

Data license

Creative Commons License