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:

  1. cluster - needs to match labelField in cellbrowser.conf.
  2. gene - can be a gene symbol or Ensembl gene ID, with or without the version.
  3. 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.