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authorPjotr Prins2022-12-03 17:29:19 -0600
committerPjotr Prins2022-12-03 17:29:19 -0600
commit5624d53264fa03b970e9fe8c61c6b7b88a01b766 (patch)
treefaf1c60663801e061eb0e6359211297ca375768d
parent89304bfdddb004a60a600f0f9436269dbea3318e (diff)
downloadgn-gemtext-5624d53264fa03b970e9fe8c61c6b7b88a01b766.tar.gz
Found publications that use search in GeneNetwork
-rw-r--r--topics/features/genenetwork/.gitignore1
-rw-r--r--topics/features/genenetwork/search.gmi6
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+contrib
diff --git a/topics/features/genenetwork/search.gmi b/topics/features/genenetwork/search.gmi
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@@ -11,13 +11,19 @@ More powerful queries will narrow down on field in the result table. For example
Example search terms:
+```
species:mouse BRCA2 - looks good, has Liver
species:mouse Tissue:Liver - 0 results
species:mouse tissue:Liver - 0 results
brca - only renders 2 results, why not BRCA2?
+```
Keywords like tissue appear to be case sensitive. Should not be the case.
+GeneNetwork search functionality is used in the publication `Integrative Functional Genomics for Systems Genetics in GeneWeaver.org`. The authors present their webservice by searching for a "nociception" QTL in a region on chromosome 4 found in GN. They export the details and use it for further analysis in GeneWeaver\cite{bubier2016}.
+
+In the publication `Systems Genetics of Obesity` GeneNetwork search is used to find genes contributing to collagen content in adipose tissue in the BXD and find similar cis-eQTL connected with adipose tissue that exist in other studies hosted on GN\cite{brockmann2016}.
+
In the paper `New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork' the authors reanalyzed an older experimental data in the GeneNetwork database.
They discovered QTLs on mouse chromosomes 3, 5, 9, 11, and 14, not found in the original study
and found new candidate genes included Slitrk6 and Cdk14. Slitrk6, in a Chromosome14 QTL for locomotion, was found to be part of a co-expression network involved in voluntary movement and associated with neuropsychiatric phenotypes. Cdk14, one of only three genes in a Chromosome5 QTL, is associated with handling induced convulsions after ethanol treatment, that is regulated by the anticonvulsant drug valproic acid\cite{PMC9024903}.