Table 1 Databases and software used in miRNA analysis
Database or software | Principal applications | Additional features | Search by |
|---|---|---|---|
miRBase (http://microrna.sanger.ac.uk/ or http://www.mirbase.org/) | miRNA target identification | Links to databases and software, such as miRanda | Accession number, name, keyword tissue, sequence PubMed ID |
miRanda (http://microrna.org) | Identification of target genes or targeting miRNA. miRNA expression profile and distinguish conserved and non-canonical sites | Support vector regression (SVR) algorithm to determine level of gene down-regulation. | miRNA, target gene |
TarBase (http://microrna.gr/) | miRNA target identification | Â | miRNA |
miR2Disease (http://www.miR2Disease.org) | Associate human diseases with specific miRNA dysregulation | Uses TarBase | Specific miRNA, disease name, tissue or target gene |
TransmiR (http://cmbi.bjmu.edu.cn/transmir) | Identify transcription factors that regulate specific miRNA | Links to NCBI gene and protein data and literature | Transcription factor names, miRNA name, species, regulation type, literature |
miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) | Document experimentally confirmed miRNA-target interactions | Provides method of interaction confirmation, information on mature miRNA and precursor, expression profile, gene target network | Species, miRNA, target gene combination |