Release Notes - DAnCER

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.

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.

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.

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.

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.

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.

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!

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.

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

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).

Release Notes - DAnCER - Wodak Lab