DASHR – a database of small human noncoding RNAs

Small non-coding RNAs (sncRNAs) are highly abundant RNAs, typically <100 nucleotides long, that act as key regulators of diverse cellular processes. Although thousands of sncRNA genes are known to exist in the human genome, no single database provides searchable, unified annotation, and expression information for full sncRNA transcripts and mature RNA products derived from these larger RNAs.

Here, researchers from the University of Pennsylvania present the Database of small human noncoding RNAs (DASHR). DASHR contains the most comprehensive information to date on human sncRNA genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). Currently, DASHR (v1.0) integrates 187 smRNA high-throughput sequencing (smRNA-seq) datasets with over 2.5 billion reads and annotation data from multiple public sources. DASHR contains annotations for ∼48 000 human sncRNA genes and mature sncRNA products, 82% of which are expressed in one or more of the curated tissues.

rna-seq

(A) Schematic diagram showing the relationship between a sncRNA gene and its mature products using miRNA gene as an example. (B) Number of annotations for sncRNA genes (left) and mature sncRNA products (right) in DASHR. (C) Number of samples and studies present for each human body system in DASHR. In total, DASHR contains over 180 high-throughput smRNA-seq datasets with over 2.5 billion processed reads. (D) Annotated mature sncRNA products with expression levels in DASHR.

Availability – DASHR is available at http://lisanwanglab.org/DASHR

Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS. (2015) DASHR: database of small human noncoding RNAs. Nucleic Acids Res [Epub ahead of print]. [article]

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