RAIN: RNA–protein Association and Interaction Networks (v1.0)
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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 | ||||||
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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 |
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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.gzThe 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 | |||
... | ... | ... | ... |