Annotate Genes¶
When you load a basic set of marker genes into your cell browser, they will be
imported as gene symbols along with an associated score, with no extra
annotations. To make the list of markers genes more useful, you can add extra
annotations using the cbMarkerAnnotate
tool. This tool will add information
about in other resources that describe gene expression profiles
(Allen Brain Atlas), diseases they have been linked to (OMIM, HPO, Sfari), and
protein class (HPRD).
Running this script on your marker genes file is very simple:
cbMarkerAnnotate inFname outFname
The format for inFname
is the same as for standard cell browser marker gene
files, a tsv or csv table with at least three columns, in this order:
- cluster - needs to match
labelField
incellbrowser.conf
. - gene - can be a gene symbol or Ensembl gene ID, with or without the version.
- score - scores are typically “avg_diff” or “p-Value” or similar. Gene
cbMarkerAnnotate
will map Ensembl gene IDs to symbols and then lookup various
gene-related databases to add more columns to inFname
and write the result to
outFname
. You can then change the marker genes file described by the markers
parameter in your cellbrowser.conf
to point to outFname
.
You can also add your own annotations (e.g. number of associated PubMed articles) to
your marker genes files. These will be displayed alongside any other annotations
that you may have added using cbMarkerAnnotate
.