Hi all,
I'll be moving out to the Bay area soon to work for Amazon, so quite a shift in my career path. There is a project I was working on that I didn't get as far as I would like but thought I would share with the group in case it could be of some use or interest. I'll try to continue developing it but probably as a weekend warrior project . . .
Basically, it searches Pubmed abstracts for genes and variants that are associated with your search term, taking a market basket analysis approach (e.g. abstracts that contained Gout also contained the gene SLC2A9). For example, if you enter cutis laxa, it will give you a ranked list of genes and variants that co-occur with that term. You can even use wildcards in the search (such as alzheimer* ) or compound queries, such as the following
"Lynch syndrome" OR "hereditary non-polyposis colorectal cancer" OR "HNPCC" OR "familial adenomatous polyposis" OR "MUTYH-associated polyposis" OR "hereditary diffuse gastric cancer" OR "Cowden syndrome" OR "Li-Fraumeni syndrome" OR "Peutz-Jeghers syndrome" OR "Muir-Torre syndrome" OR "Turcot syndrome" OR "Juvenile Polyposis syndrome"
This returns 49 genes, 13 of which correspond to the 13 genes on the ColoSeq panel, and 8 of those 13 are in my top 10 ( http://web.labmed.washington.edu/tests/genetics/COLOSEQ ).
By clicking on a gene or variant, you can also see the supporting papers.
I see this as being able to help (1) choose genes for a panel, (2) annotate genes with variants from the literature, and (3) identify genes that one might want to scrutinize especially carefully when studying a particular disease.
Let me know your trials and tribulations with this search engine.
Thanks! And I hope to meet some of you guys and gals when I get out there.
Justin
I'll be moving out to the Bay area soon to work for Amazon, so quite a shift in my career path. There is a project I was working on that I didn't get as far as I would like but thought I would share with the group in case it could be of some use or interest. I'll try to continue developing it but probably as a weekend warrior project . . .
Basically, it searches Pubmed abstracts for genes and variants that are associated with your search term, taking a market basket analysis approach (e.g. abstracts that contained Gout also contained the gene SLC2A9). For example, if you enter cutis laxa, it will give you a ranked list of genes and variants that co-occur with that term. You can even use wildcards in the search (such as alzheimer* ) or compound queries, such as the following
"Lynch syndrome" OR "hereditary non-polyposis colorectal cancer" OR "HNPCC" OR "familial adenomatous polyposis" OR "MUTYH-associated polyposis" OR "hereditary diffuse gastric cancer" OR "Cowden syndrome" OR "Li-Fraumeni syndrome" OR "Peutz-Jeghers syndrome" OR "Muir-Torre syndrome" OR "Turcot syndrome" OR "Juvenile Polyposis syndrome"
This returns 49 genes, 13 of which correspond to the 13 genes on the ColoSeq panel, and 8 of those 13 are in my top 10 ( http://web.labmed.washington.edu/tests/genetics/COLOSEQ ).
By clicking on a gene or variant, you can also see the supporting papers.
I see this as being able to help (1) choose genes for a panel, (2) annotate genes with variants from the literature, and (3) identify genes that one might want to scrutinize especially carefully when studying a particular disease.
Let me know your trials and tribulations with this search engine.
Thanks! And I hope to meet some of you guys and gals when I get out there.
Justin