snoDB

Help page


This page contains short descriptions pertaining to every aspect of the snoDB web application.


Clicking on the logo will always bring you back to snoDB's main page.


Search Engines


The "Gene search" tab features two search engines while the remaining tabs only feature the first:

Search by Keyword

Entering a search term returns all entries featuring the supplied term. The field drop-down menu restricts the query to a single column corresponding to the selected field.

Search by Position

Searches the database restricting to snoRNAs at the specified positions. A blank start is considered as "Anything under end position" and a blank end is considered as "Anything above start position". The query will be filtered to solely return entries between the supplied values. The "Chromosome" drop-down menu can be used to further restrict the query.


Results


Results are specific to each tab:

Gene Search

Displays basic information on snoRNAs contained within snoDB. Ensembl IDs are provided to differentiate between snoRNAs with the same name but from different genomic loci or with different recorded lengths.

Gene symbols in the "Results" tables are clickable and lead to a page which displays all available information in snoDB relating to the gene clicked on:


  • Gene Summary
  • Reiterates much of the information found in its parent tab, though in a more compact format, while adding the sequence of the particular snoRNA according to Ensembl along with links to a potential host gene and a link to the RISE: RNA Interactome database* when available.

  • ID Links
  • Many different nomenclatures are used to refer to a same snoRNA and so this section aims to provide an easy way for users to obtain information on a given snoRNA no matter what identifier it may have on different platforms. To this effect, links to various sources are provided where applicable.

  • Associated Target(s)
  • Shows which targets, if any, a given snoRNA guides the modification of. All sources, listed as numbers linked to explicit citations in the reference section below, are clickable and lead to the articles from which the target data was extracted or, in the case of targets pulled from snoRNAbase, to the snoRNAbase website.

  • RNA-Seq Expression
  • Displays transcriptomic data for the selected gene in various cell lines. Explicit cell line descriptions may be viewed by hovering over the grey "?" next to the column names. For a brief overview of the pipeline used to acquire the expression data, see the Experiment details page.

  • Accumulation
  • Shows (when available) a graph of accumulation data in Counts per millions (CPM) obtained through the sequencing of various cell lines.


    ID Conversion

    This tab allows users to quickly search for IDs associated to genes on the following platforms: Ensembl, Hugo Gene Nomenclature Committee (HGNC), Genome Browser(UCSC), NCBI (Refseq) and Rfam.

    snoRNA Target

    It is well established that snoRNAs guide the modification of selected sites in rRNA with impacts pertaining to ribosome biogenesis, but recent studies have shown a much wider array of possible interactions and modifications with potential roles in alternative splicing, the regulation of chromatin architecture and the regulation of pre-mRNA stability. Hence, this section pools target data from various studies to showcase the evergrowing number of snoRNA interactions and makes them easily searchable.


    Displayed Fields


    The displayed fields can be dynamically changed by clicking on the boxes that populate this section. Doing so determines which fields are visible in 'Results'. These changes are applied without refreshing an active query. Users should be aware that rows may seem duplicated if they only have different values in hidden fields.


    References


    - Aken, B.L., et al. (2017) Ensembl 2017, Nucleic Acids Res, 45, D635-D642.
    - Deschamps-Francoeur, G., et al. (2017) CoCo: read assignment correction for embedded and multimapped genes, under review.
    - Deschamps-Francoeur, G., et al. (2014) Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency, Nucleic Acids Res, 42, 10073-10085.
    - Gumienny, R., et al. (2017) High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq, Nucleic Acids Res, 45, 2341-2353.
    - Kehr, S., et al. (2014) Matching of Soulmates: coevolution of snoRNAs and their targets, Molecular biology and evolution, 31, 455-467.
    - Krogh, N., et al. (2016) Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity, Nucleic Acids Res, 44, 7884-7895.
    - Lestrade, L. and Weber, M.J. (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs, Nucleic Acids Res, 34, D158-162.
    * - Gong J, Shao D, Xu K, et al. RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Res. 2017.
    - Nawrocki, E.P., et al. (2015) Rfam 12.0: updates to the RNA families database, Nucleic Acids Res, 43, D130-137.
    - Yates, B., et al. (2017) Genenames.org: the HGNC and VGNC resources in 2017, Nucleic Acids Res, 45, D619-D625.


    Contact Us


    This web interface was developped by trainees in the Scott group: Darren.Mathurin-St-Pierre@USherbrooke.ca and Philia Bourelle-Bouchard. For any general questions or comments about the snoDB web application, contact Philia at: Philia.Bourelle-Bouchard@yandex.com



    The principal investigator Michelle Scott and the team behind the data curation can be contacted at: Michelle.Scott@USherbrooke.ca