Hi everyone. I'm still new to the kinds of analysis I have been doing and would appreciate a second opinion to verify my approach.
I have mass spec protein expression data obtained under various experimental conditions. In an earlier thread I was figuring out how to represent this data visually and I got some great suggestions; I eventually chose to use Cytoscape to map the proteins to GO terms and make an enriched network. Now that I can pull a bunch of genes out of various related GO categories, I want to compare them to gene databases for known genes associated to a particular disease. Let's use Autism as an example.
Using databases for autism-related genes such as SFARI, am able to pull out a gene list and then compare it to the list of genes that I got from my mass spec data. The point of this is to verify our experimental approach to show that our data - though not experimentally confirmed for a particular gene - can be used as a tool to narrow in on genes of interest for various diseases to give a direction for researchers to look (it's a bit more complicated than that but that is the general idea).
Question 1: Is my overall approach of simply comparing a list of putative autism-related genes to our dataset valid? Is there any pitfall to this kind of approach I should be aware of?
Question 2: Not all genes in a particular database may be the best candidates for that diseases. One example of this is this Alzheimer's database which has ~500 genes. However, they have a top 10 list. Is it better to compare my genes with the entire database or just the top 10?
Question 3: All of the genes I have are from rats. Some of the gene lists have a mixture of different model organisms. Is it valid to cross-compare genes between model organisms? I understand that the data I have is not verified by other experimental approaches, but in terms of leading research in a particular direction, is it okay to compare disease-related genes across species like this?
Question 4: There are sometimes multiple databases out there for a particular disease. How do I decide which ones to use for my comparison? Are some better than others? How do I figure out something like this?
Any basic information or clarification would greatly be appreciated. I just want to be very careful so I'd appreciate a second opinion. Thank you.