Alzheimer's Disease and Reconstruction of Networks

Question

[aaaburak20]

I am just experiencing an internship in a Bioinformatics and Medical informatics laboratory. I am doing some studies about alzheimer's disease.

I have about 250 genes which are told to be related with AD. I got these genes from different network databases from different networks. I want to reconstruct new networks with these genes but there are lots of genes which are told to be related with the disease. How can I check these genes' level of relevancy with AD? So that I can decrease the number of genes that I will build new networks with.

Answer 1

[Denise CS]

Check the data in the Open Targets Platform. You can search either search for the disease entity (i.e. Alzheimers disease) or the genes you've got. The association between diseases and genes in this platform is based on integrating evidence from different databases including the GWAS catalog (suggested by Floris Brenk), UniProt, Reactome (biological pathways), Europe PMC (for text mining), animal models. The current version of our platform lists 271 genes associated with that Alzheimers taking into account genetic variants only (from GWAS, UniProt and EVA). You can filter those very easily for example to show associations based on UniProt data which gives you one gene, SORL1, or EVA which gives you five genes including the well known APOE. The platform provides you with an association score for all pieces of evidence combined. The gene with the highest association based on this integrated data is PSEN1. You can then explore PSEN1 itself such as view the protein structure of its translation For more details, check our 'Platform documentation' page.

[aaaburak20]

so, I can decide for a specific threshold for the scores that this platform gives for each gene for the disease and decide which genes are more relavant with Alzheimer's. How can I see the references for each gene's scores?

[Denise CS]

You can look at the evidence for each gene from which we derive the scores, and see references if they are available. For PSEN1 this is the evidence we've got for the association with AD. Explore the different pieces of evidence, e.g. Genetic associations and get the references from there. Does this make sense?

[aaaburak20]

this makes sense, thanks for your help!

Answer 2

[Floris Brenk]

GWAS -> http://www.ncbi.nlm.nih.gov/pubmed/24162737 is a way...