From 191fb9b0e899051fd22fcc9c918bcd28ef545f23 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 17 Nov 2021 08:14:55 -0600 Subject: story board --- story-boards/starting-from-known-gene/generate.sh | 10 +++++++- story-boards/starting-from-known-gene/genewiki.png | Bin 148494 -> 148494 bytes .../starting-from-known-gene/global-search.png | Bin 12151 -> 12151 bytes .../starting-from-known-gene/search-brca2.png | Bin 0 -> 62874 bytes story-boards/starting-from-known-gene/search.png | Bin 0 -> 45235 bytes story-boards/starting-from-known-gene/search1.png | Bin 0 -> 34546 bytes story-boards/starting-from-known-gene/search2.png | Bin 0 -> 45235 bytes .../starting-from-known-gene.md | 27 +++++++++++++++++++-- .../trait-1419076_a_at.png | Bin 0 -> 99233 bytes 9 files changed, 34 insertions(+), 3 deletions(-) create mode 100644 story-boards/starting-from-known-gene/search-brca2.png create mode 100644 story-boards/starting-from-known-gene/search.png create mode 100644 story-boards/starting-from-known-gene/search1.png create mode 100644 story-boards/starting-from-known-gene/search2.png create mode 100644 story-boards/starting-from-known-gene/trait-1419076_a_at.png (limited to 'story-boards') diff --git a/story-boards/starting-from-known-gene/generate.sh b/story-boards/starting-from-known-gene/generate.sh index c5d4d3d..c44558e 100755 --- a/story-boards/starting-from-known-gene/generate.sh +++ b/story-boards/starting-from-known-gene/generate.sh @@ -1,10 +1,18 @@ #!/bin/bash -ruby ../../scripts/screenshot.rb --url "http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2" --out genewiki.png --extract 1200x500+0+0 +ruby ../../scripts/screenshot.rb --out trait-1419076_a_at.png --url "https://genenetwork.org/show_trait?trait_id=1419076_a_at&dataset=HC_M2_0606_P" exit 1 + +ruby ../../scripts/screenshot.rb --out search-brca2.png --extract 1200x330+0+330 --url "https://genenetwork.org/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=BRCA2&search_terms_and=&FormID=searchResult" + +ruby ../../scripts/screenshot.rb --url "http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2" --out genewiki.png --extract 1200x500+0+0 + ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/" --out genenetwork-home.png convert -extract 800x100+0+0 genenetwork-home.png global-search.png +convert -extract 570x350+0+90 genenetwork-home.png search1.png +convert -extract 570x500+0+90 genenetwork-home.png search.png + ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/gsearch?type=gene&terms=Brca2" --out global-search-gene.png --extract 800x300+0+0 diff --git a/story-boards/starting-from-known-gene/genewiki.png b/story-boards/starting-from-known-gene/genewiki.png index 22d7580..eb90846 100644 Binary files a/story-boards/starting-from-known-gene/genewiki.png and b/story-boards/starting-from-known-gene/genewiki.png differ diff --git a/story-boards/starting-from-known-gene/global-search.png b/story-boards/starting-from-known-gene/global-search.png index b2cf1ef..90841ad 100644 Binary files a/story-boards/starting-from-known-gene/global-search.png and b/story-boards/starting-from-known-gene/global-search.png differ diff --git a/story-boards/starting-from-known-gene/search-brca2.png b/story-boards/starting-from-known-gene/search-brca2.png new file mode 100644 index 0000000..e08f67d Binary files /dev/null and b/story-boards/starting-from-known-gene/search-brca2.png differ diff --git a/story-boards/starting-from-known-gene/search.png b/story-boards/starting-from-known-gene/search.png new file mode 100644 index 0000000..ce286e7 Binary files /dev/null and b/story-boards/starting-from-known-gene/search.png differ diff --git a/story-boards/starting-from-known-gene/search1.png b/story-boards/starting-from-known-gene/search1.png new file mode 100644 index 0000000..f324d52 Binary files /dev/null and b/story-boards/starting-from-known-gene/search1.png differ diff --git a/story-boards/starting-from-known-gene/search2.png b/story-boards/starting-from-known-gene/search2.png new file mode 100644 index 0000000..8e05ef4 Binary files /dev/null and b/story-boards/starting-from-known-gene/search2.png differ 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: [![Genewiki](./genewiki.png "Genewiki for Brca2")](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 + +[![GN Search1](./search1.png "Genenetwork search1")](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 + +[![BRCA2](./search-brca2.png "BRCA2")](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 + +[![1419076_a_at](./trait-1419076_a_at.png "1419076_a_at")](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 diff --git a/story-boards/starting-from-known-gene/trait-1419076_a_at.png b/story-boards/starting-from-known-gene/trait-1419076_a_at.png new file mode 100644 index 0000000..ecd3013 Binary files /dev/null and b/story-boards/starting-from-known-gene/trait-1419076_a_at.png differ -- cgit v1.2.3