2016: predicting miRNA-disease associations with a vector space model.

Data associated with the article:

Pasquier, C., and Gardès, J. (2016), Prediction of miRNA-disease associations with a vector space model. Scientific reports, Nature Publishing Group, 6, 27036.

Data sources

The method is based on the analysis of the following ressources:

• experimentally verified miRNA-disease associations retrieved from human miRNA-disease database (HMDD) v2.0 [1]
• standard disease names included in the Medical Subject Headings (MeSH) terms
• experimentally validated miRNA-mRNA interaction, downloaded from miRTarBase [2]
• family, genomic location and textual description of miRNAs stored in miRBase [3]
• abstract of research papers associated with every miRNA stored in miRBase retrieved from Pubmed

Results

• Supplementary Table S1 Average AUC obtained on 83 diseases
• Supplementary Table S2 list of 86 associations included in HMDD that obtain a significant score of invalidation
• Supplementary Table S3 AUC scores obtained for the 15 important diseases using the updated database
• Supplementary Table S4 AUC scores obtained for all the diseases using the revised reference database
• Supplementary Table S5 List of 126 potential new associations between miRNAs and diseases identified by MiRAI using the revised reference database (confirmed associations are highlighted in green)
• Supplementary Table S6 List of 72 putative new associations that need to be confirmed

Generated data

• mirna_descriptions.zip miRna descriptions specified in MirBase
• mirna_mirbase_abstracts.zip abstracts of PubMed articles associated with miRNAs in MirBase
• mirna_abstracts.zip abstracts of PubMed articles associated with miRNAs (automatically retrieved by parsing the abstracts)
• Updated Reference database The manually curated database of miRNA-disease associations, obtained as described in the paper

References

[1] Li, Y. et al. HMDD v2.0: A database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 42, 1070–1074 (2014).

[2] Hsu, S. D. et al. MiRTarBase: A database curates experimentally validated microRNA-target interactions. Nucleic Acids Research 39, 163–169 (2011).

[3] Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A. & Enright, A. J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic acids research 34, D140–D144 (2006).