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.
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 
- standard disease names included in the Medical Subject Headings (MeSH) terms
- experimentally validated miRNA-mRNA interaction, downloaded from miRTarBase 
- family, genomic location and textual description of miRNAs stored in miRBase 
- abstract of research papers associated with every miRNA stored in miRBase retrieved from Pubmed
- 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
- 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
 Li, Y. et al. HMDD v2.0: A database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 42, 1070–1074 (2014).
 Hsu, S. D. et al. MiRTarBase: A database curates experimentally validated microRNA-target interactions. Nucleic Acids Research 39, 163–169 (2011).
 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).