Release Notes - DAnCER - Wodak Lab

Version 2.3 — 2012 April

  • Update data from NCBI Gene, UniProt, PFam, iRefWeb, Gene Ontology, gene disease information, ExPASy, Ensembl, and more.
  • Add ChIP-seq data for select genes.
  • Label transcription factors.
  • Categorize CM genes by epigenetic role (searchable).
  • Search by chromosome.
  • Add new CM evidence (and upgrade previous evidence).
    • Many new confirmed and putative CM genes.
    • CM genes confirmed by GO annotations labelled as such.
    • Putative status by homology now split into 3 distinct groups:
      • Has direct homolog that is a known (confirmed) CM gene,
      • Has distant homolog (transitive closure) that is a known (confirmed) CM gene,
      • Has distant homolog (transitive closure) that is only a putative CM gene, by some other evidence than homology.

Version 2.2 — unreleased

  • Show top-level MeSH categories for each human gene's neighbourhood.
  • Label enriched MeSH categories in a gene's neighbourhood.
  • Better and clearer interactions display.
  • Homologs section on gene page shows link to homolog's gene page, and link to evidence.

Version 2.1 — 2011 October

  • Better support for GO ontologies (ie. biological_process, molecular_function, and cellular_component):
    • Choose which ontology to use when searching for GO term filters;
    • GO terms categorized by type in gene pages.
  • Some GO terms categorized as CM:
    • Show only CM-related GO terms when searching for GO term filters;
    • CM-related GO terms highlighted on Gene page.

Version 2.0-beta — 2011 July

  • Enzymatic function (EC Numbers) for proteins (from ExPASy) is now included.
  • Genes annotated with diseases using MeSH terms now.
  • Search for CM genes by:
    • Enzymatic function
    • Related disease
    • Annotated GO Terms
    • CORUM Complexes
  • New customizable exporter of search results.
  • Better Gene ID List disambiguation and clean-up.

Version 1.6 — 2011 February

  • Better integration with the Gene Ontology (GO):
  • Search by GO terms annotated to genes.
    • Create a list using search box or paste term list manually.
    • Restrict to only genes who were annotated with term with experimental evidence.
  • Find relevant GO terms to search on by using search box to locate terms of interest to search by.
    • Search terms can be term names, synonyms, GO accessions, or related keywords.
    • Restrict by ontology (cellular component, biological process, or molecular function).
  • GO annotations now listed on each gene page by default.
    • Includes term accession, name, definition and the evidence code(s) for the annotation.
    • Can hide non-experimental terms if the list is large.

Version 1.5 — 2010 December

  • Switched to a search query format that is simpler, but better orders results by relevance.
  • Gene ID file upload widget is less obstrusive, integrates better with other filters/facets and works asynchronously (no page reload required) in FF, Chrome, Safari, and Opera.
  • Fixed problems with visual inconsistencies, text clipping, and some display issues in Safari.

Version 1.4 — 2010 October

  • Overhauled how searching and faceting for genes works, allowing more flexibility in searching.
  • Can now choose how multiple facets for a single field are searched (eg. all, any, or none).
  • Filters/facets now grouped into different tabs by default.
  • "DAnCER: disease-annotated chromatin epigenetics resource." is published!

Version 1.3 — 2010 August

  • Added new Statistics page for a quick overview of the data provided by DAnCER.
  • PDB hit table shows blanks when there are no hits, rather than 0 (removes visual clutter).
  • Search results table lists all gene IDs available now, though shows only 1 by default, unless list is expanded.

Version 1.2 — 2010 July

  • PDB hits in PDB count table are reported as totals per species, instead of per structure, enhancing readability.
  • Each gene now lists diseases associated with its neighbours on its gene page (as well as its own diseases).
  • Added more genes to DAnCER and promoted some more genes' CRM status to Confirmed.
  • Added new gene menus for search results to provide easier access to:
    • Searching for a gene's homologs in DAnCER
    • Searching for a gene's neighbours in DAnCER
    • Bringing up the gene's and its protein products' interaction graph in Netility

Version 1.1 — 2010 June

  • Search results now in table format with sortable columns.
  • Columns in search results give a summary of that field's statistics (min, max, mean, etc.)
  • More information is displayed in the search results (eg. neighbour and neighbour disease counts).

Version 1.0 — 2010 March

  • DAnCER 1.0 is released
DAnCER 2.3
Disease Annotated Chromatin Epigenetics Resource
Watch a webinar (or browse the slides) on how to use DAnCER here.