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DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.

TitleDASHR 2.0: integrated database of human small non-coding RNA genes and mature products.
Publication TypeJournal Article
Year of Publication2019
AuthorsKuksa PP, Amlie-Wolf A, Katanić Ž, Valladares O, San Wang L-, Leung YYee
Date Published2019 03 15
KeywordsDatabases, Nucleic Acid, Genomics, Humans, RNA, Long Noncoding, RNA, Small Untranslated, Sequence Analysis, RNA, Software

MOTIVATION: Small non-coding RNAs (sncRNAs, <100 nts) are highly abundant RNAs that regulate diverse and often tissue-specific cellular processes by associating with transcription factor complexes or binding to mRNAs. While thousands of sncRNA genes exist in the human genome, no single resource provides searchable, unified annotation, expression and processing information for full sncRNA transcripts and mature RNA products derived from these larger RNAs.
RESULTS: Our goal is to establish a complete catalog of annotation, expression, processing, conservation, tissue-specificity and other biological features for all human sncRNA genes and mature products derived from all major RNA classes. DASHR (Database of small human non-coding RNAs) v2.0 database is the first that integrates human sncRNA gene and mature products profiles obtained from multiple RNA-seq protocols. Altogether, 185 tissues/cell types and sncRNA annotations and >800 curated experiments from ENCODE and GEO/SRA across multiple RNA-seq protocols for both GRCh38/hg38 and GRCh37/hg19 assemblies are integrated in DASHR. Moreover, DASHR is the first to contain both known and novel, previously un-annotated sncRNA loci identified by unsupervised segmentation (13 times more loci with 1 678 800 total). Additionally, DASHR v2.0 adds >3 200 000 annotations for non-small RNA genes and other genomic features (long-noncoding RNAs, mRNAs, promoters, repeats). Furthermore, DASHR v2.0 introduces an enhanced user interface, interactive experiment-by-locus table view, sncRNA locus sorting and filtering by biological features. All annotation and expression information directly downloadable and accessible as UCSC genome browser tracks.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Pubmed Link
Alternate JournalBioinformatics
PubMed ID30668832
PubMed Central IDPMC6419920
Grant ListU54 AG052427 / AG / NIA NIH HHS / United States
R01 GM099962 / GM / NIGMS NIH HHS / United States
U01 AG032984 / AG / NIA NIH HHS / United States
T32 AG000255 / AG / NIA NIH HHS / United States
UF1 AG047133 / AG / NIA NIH HHS / United States
U24 AG041689 / AG / NIA NIH HHS / United States

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