Storyboard: starting from a known gene

GeneNetwork contains data on thousands of experiments. How do you mine GN when you have the name of a gene? Start with BRCA2.

Use the search page

The top bar of GeneNetwork shows a global search:

We can look for the Brca2 mouse gene, resulting in

FIXME: @zsloan above image should show a table of results too, see https://github.com/genenetwork/genenetwork2/issues/629

Find the right alias/name

GeneNetwork knows about aliases. But sometimes you want to check what aliases there are in mouse. If you search for BRCA2 and click on a search result, for example for 1448542_at, you get to the 'trait page' which shows the aliases:

GeneNetwork ignores case by default. In a search use quotes to search case sensitive. For example, BRCA2 on wikidata.org refers to the human gene. The mouse gene is named Brca2.

Find the GeneNetwork genewiki entry

GeneNetwork maintains info on gene entries. For example on the above trait page for 1448542_at/BRCA2 the [genewiki] button takes you to:

FIXME: @zsloan we aim to move this functionality to GN2/markdown

Looking experiments that

On the GN home page we find advanced search routines

In the 'Get any' box type `BRCA2' and hit [Search] to find all traits that mention Brca2 for the matching datasets (here Hippocampus mRNA) resulting in

So, for this dataset 7 results are shown with interesting QTL scores.

Click on the trait 1419076_a_at that is annotated as Brca2 on Chr5: 150.569266 with a QTL on Chr1: 191.908117 and we get to the powerful mapping page

As we picked this trait from an RNA dataset 1419076_a_at likely is a gene expression trait. Clicking on link [Hippocampus Consortium M430v2 (Jun06)] tells us is is a dataset on 'Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource.'

FIXME: @pjotrp: add a link out on the mapping page to wikidata FIXME: @pjotrp: [UCSC] link is pointing to CHR12 FIXME: @pjotrp: we need a link to uniprot(!)

TODO

[ ] expand story line
[ ] global search is faulty, see gn-gemtext-threads/issues/genenetwork/global-search.gmi
[ ] migrate GeneWiki entries