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		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