How To Find Special Function Of Gene In My Different Genes

Question

[Haoboli]

Hi,I am new to gene ontology analysis and i need help for the following question: i used fold change to find my different genes in Microsoft excel, then i get the annotation for the different genes, here comes the problem, the next step i should would be do gene ontology analysis,right?and if i would like to find genes which involve in special function, such as "lipid", how can i do that? Detail with example will be appreciated.

[Laurent]

You write that you found "different expression genes by fold change". Does that mean that you have not applied any stats to get your genes of interest? If you have replicates, I would strongly advise to do it now, before investing time in downstream analysis and possibly other validation experiments.

[Haoboli]

Dear Laurent, Thank you for your comment. Yes, I have not applied any stats to get my genes of interest, because I have no idea how to find it. For example, I would like to find genes in the different expression genes(I have found these by fold change: Signal of Treatment group/ signal of Control group) which are involve in "lipid metabolism", would you kindly give me some guidance?

[Haoboli]

The main purpose of my experiment is to find out effect of different treatments on genes expression which involved especially in lipid metabolism, therefore, i think i should first find out different expression genes between groups, and then do the GO analysis and find genes whit this function by GO term, the problem is i don't know how to do this in bioconductor?or what i think is not right?

Answer 1

[Laurent]

Dear HaoboLi,

I think you might want to try to fix your general analysis and do some reading to familiarise yourself with the background and technology. If you want to use Bioconductor, which I would advise, have a look at the Bioconductor page. There is a lot of documentation available there as well as on many other places on the web. This one, by Thomas Girke, UC Riverside, is also very helpful. It includes, among others, sections about the 'Analysis of Differentially Expressed Genes' and 'Gene Ontologies'.

Regarding your analysis pipeline, have a look at the Using Bioconductor for Microarray Analysis page and references therein as a starting point. The book Bioconductor Case Studies will provide all you need to know and much more.

Hope this helps.

Answer 2

[Qdjm]

What you are trying to do is called an over-enrichment analysis, over-representation analysis or a functional enrichment test. There are a lot of web-based tools for doing this.

One of the most popular is DAVID. The interface is a little bit hard to understand but its very powerful. There's a Nature Protocol paper that may help you.