What Phenotype databases do you recommend for searching genes related to diseases?

Question

[gjespitia]

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.

Answer 1

[Pratik]

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!

[gjespitia]

Thank you so much, this database has much more than the others combined!

Answer 2

[ellimilial]

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:
  • https://biokeanos.com/search?q=%2Bdisease+gene