How to start Gene Analysis?

Question

[Pranavathiyani G]

I have a gene list(only Gene Symbol), how can I analyse or find something with it (E.g.,: Pathways involved, Mutation Frequency, Interaction network, etc) and How can I interpret their relationship among the other genes?

What are the ways to do study a set of genes?

E.g.,

ADARB1
ADPRH
PARP1
AGTR1
AHR
AIF1
AKR1B1
ALOX15
ALOX15B
ALPL
AMH
BIN1

Answer 1

[Omid]

I recommend GeneMANIA www.genemania.org) if you want to see the biological connections among your genes. you can see pathway.proteion-protein interactions, gene interaction, co-expression, co-localization.

the other database which might be helpful for you is GeneCards ( www.genecards.org) if you work on human. When you give one gene as input you will have a lot of information about that gene like alternative names of that gene ,gene function, GO terms, network, interaction with drug, disease...

Answer 2

[Amitm]

hi

First be clear with your hypothesis. What sort of experiment/ analysis gave you that gene list at the first place. Once there, start with gene ontology (GO) analysis. If you aren't aware with GO, its hierarchically organized set of annotation terms for any given gene. Look at the linked website for more details. There are many online tools to do GO analysis. More or less everyone has the same backend data (from GO consortia) and then a set of statistical tests are applied to check if your gene set is enriched/ depleted for a particular 'functional' term. A very coarse e.g. - lets say the human genome has 10% of its genes belonging to process X. But in your list 50% of genes belong to that process.

DAVID is one web-resource to start with for GO analysis. There are help pages there.

Some caveats - 1) If your gene list is small, no process might come out to be statistically significant. Thats just statistics 2) If you have a large gene list, there is high probability that you might get some processes significant. That might/ might not be relevant.

[Jean-Karim Heriche]

As far as I can tell DAVID data sources haven't been updated in ~7 years (the most recent update listed is GO from December 2009). I wouldn't use such outdated data for anything. A lot of genes got new annotations/functions in that time.

[Amitm]

Thanks for pointing it out. It had never occurred to me to cross-check their database version. Had assumed their "2003-2016" quote on landing page meant something. Anyways, on smaller gene lists I complement my search with GeneMania or String. Or, I would download BioGrid release and parse it for my query gene list interacting neighbours (1st degree or more).

Will have to now find another GO analysis tool :-( Checked with ToppGene and PantherDb. Both seemed updated with recent releases of GO. But will dig deeper to be sure.

[GenoMax]

@Jean-Karim: I am cautiously optimistic that this is an oversight. The page you are referring to was last updated in January 2010. I have emailed DAVID team and will post an update.

Answer 3

[Jean-Karim Heriche]

On top of GeneMANIA already mentioned, there are a number of resources that allow you to explore gene lists e.g. Pathway Commons, Reactome. You can also have a look at GSEA and there are various R packages e.g. topGO for GO terms enrichment analysis. Finally, see also this blog post.