title: DASHR: database of small human noncoding RNAs.
abstract: 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, we 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. DASHR is available at http://lisanwanglab.org/DASHR.
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Penn Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Yuk Yee
authors.initials: YY
authors.lastname: Leung
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Penn Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Pavel P
authors.initials: PP
authors.lastname: Kuksa
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Amlie-Wolf
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Otto
authors.initials: O
authors.lastname: Valladares
authors.affiliation: Penn Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Lyle H
authors.initials: LH
authors.lastname: Ungar
authors.affiliation: Penn Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Sampath
authors.initials: S
authors.lastname: Kannan
authors.affiliation: Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA bdgregor@sas.upenn.edu.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Gregory
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Penn Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA Institute on Aging, University of Pennsylvania, Philadelphia, PA 19104, USA lswang@mail.med.upenn.edu.
authors.forename: Li-San
authors.initials: LS
authors.lastname: Wang
mesh_terms: D030561:Databases, Nucleic Acid; D006801:Humans; D058977:Molecular Sequence Annotation; D012323:RNA Processing, Post-Transcriptional; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D058727:RNA, Small Untranslated