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| author | Pjotr Prins | 2021-11-17 08:14:55 -0600 |
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| committer | Pjotr Prins | 2021-11-17 08:14:55 -0600 |
| commit | 191fb9b0e899051fd22fcc9c918bcd28ef545f23 (patch) | |
| tree | 31823c1bd650b41bcb61ae7747448dcbbd81b77a /story-boards/starting-from-known-gene/starting-from-known-gene.md | |
| parent | 2e5ad9135530a2bd5d9b2730471b2e43b99cab0f (diff) | |
| download | gn-docs-191fb9b0e899051fd22fcc9c918bcd28ef545f23.tar.gz | |
story board
Diffstat (limited to 'story-boards/starting-from-known-gene/starting-from-known-gene.md')
| -rw-r--r-- | story-boards/starting-from-known-gene/starting-from-known-gene.md | 27 |
1 files changed, 25 insertions, 2 deletions
diff --git a/story-boards/starting-from-known-gene/starting-from-known-gene.md b/story-boards/starting-from-known-gene/starting-from-known-gene.md index 2abd7a1..523d4b0 100644 --- a/story-boards/starting-from-known-gene/starting-from-known-gene.md +++ b/story-boards/starting-from-known-gene/starting-from-known-gene.md @@ -26,11 +26,34 @@ GeneNetwork ignores case by default. In a search use quotes to search case sensi # Find the GeneNetwork genewiki entry -GeneNetwork maintains info on gene entries. For example for BRCA2: +GeneNetwork maintains info on gene entries. For example on the above trait page for 1448542_at/BRCA2 the [genewiki] button takes you to: [](http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2) -FIXME: we aim to move this functionality to markdown +FIXME: @zsloan we aim to move this functionality to GN2/markdown + +# Looking experiments that + +On the GN home page we find advanced search routines + +[](https://genenetwork.org/) + +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 + +[](http://genenetwork.org/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=BRCA2&search_terms_and=&FormID=searchResult) + +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 + +[](https://genenetwork.org/show_trait?trait_id=1419076_a_at&dataset=HC_M2_0606_P) + +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 |