Databases and resources for human small non-coding RNAs

In 2001, three groups published independent reports on the discovery of a new class of small non-coding RNAs (sRNAs), which were named micro-RNAs (miRNAs) [1-3]. These comprise a large family of small, ~22 nucleotide-long, non-coding RNAs that have emerged as key players in post-transcriptional gene regulation [4]. Subsequent years have witnessed the discovery of many new types of sRNAs. In humans, apart from the hundreds of miRNAs detected so far, there are also many endogenous small interfering RNAs (endo-siRNAs)[5] and piwi-interacting RNAs (piRNAs)[6,7]. These and other short non-coding RNA molecules collectively are called 'sRNAs'. They are generally short (~18-30 nucleotides [nt]); do not code for proteins; exert their function as RNA molecules generally combined with protein factors; and represent a substantial portion of the RNA output of cells. Moreover, sRNAs encompass a diverse, widespread and basal regulatory system: they are known to regulate genes and genomes at different levels, including chromatin structure, transcription, RNA stability and translation [8-10]. Furthermore, they can act as activators or inhibitors and their disruption has been linked to disease [11]. The explosion of information on sRNAs makes necessary its organisation--in terms of their biogenesis, expression properties and functional characteristics--into public databases.Traditionally, GenBank,[12] the European Molecular Biology Laboratory (EMBL)[13] and the DNA Data Bank of Japan (DDBJ)[14] have been the depository of RNA sequences, while the Gene Expression Omnibus (GEO)[15] database at the National Center for Biotechnology Information (NCBI) compiles high-throughput data for miRNAs and other sRNAs from publications. Besides these generic resources, there are specialised databases for sRNAs. The most complete ones are those related to miRNAs, since their functional role in RNA metabolism is also the best characterised [5]. The miRBase database [16] (Table 1) is considered the ce