Thank you so much, this database has much more than the others combined!
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gjespitia •
What Phenotype databases do you recommend for searching genes related to diseases?
Good afternoon I'd like to make a collection of genes related to a disease (say, leprosy), based on databases. So far I have been using:
- the Human Genome Epidemiology (HuGE) Navigator (https://phgkb.cdc.gov/HuGENavigator/startPagePhenoPedia.do)
- The Phenotype–Genotype Integrator (PheGenI, http://www.ncbi.nlm.nih.gov/gap/phegeni)
- https://www.disgenet.org/
Is there other database would you recommend? Thank you in advance for your attention.
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Okay. I think you'll like this alot. I downloaded this gene-disease pathway association database file from here: http://ctdbase.org/reports/CTD_genes_diseases.csv.gz
Here is the link so you can explore: http://ctdbase.org/downloads/#gd
I found 1918 unique genes related to Leprosy by doing the following in bash:
grep Leprosy '~/CTD_genes_diseases.csv' | cut -d ',' -f1 | sort | uniq
grep Leprosy '~/CTD_genes_diseases.csv' | cut -d ',' -f1 | sort | uniq | wc -l
1918
Good luck!
In addition to (aforementioned) CTD and DisGeNET, there's also:
- OpenTargets that itself combines several databases (including self-designed, curated studies and literature extraction, really worth a look).
- OMIM
- Depending on the direction you're interested in: either GeneCards or MalaCards
- If you are looking for more (including those that above ones aggregate), take a look here:
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