Gene Expression Analysis - Microarrays - Geneset

Question

[Krzysztof]

Hello,

I am going to analyze the expression of genes which encode proteins with KRAB domain in 2 cell types. I had found relevant microarray experiments in GEO database. I have got also gene set list with gene symbols. I have got access to GenePattern server.

I do not know how to start with this kind of analysis.

I would appreciate any help. Any other software or website?

Best, Krzysztof

Answer 1

[seidel]

If you use bioconductor as suggested by Juan, there is an easy way to test specific gene lists for differential expression using a function called geneSetTest(). It's a function in the limma library in R, also called "wilcoxGST", which computes a p-value to test the hypothesis that a selected set of genes tends to be more highly ranked in terms of a given test statistic compared to a randomly selected set of genes. (refs below)

Goeman, JJ, and Buhlmann P (2007). Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23, 980-987.

Michaud, J, Simpsonet al. (2008). Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics 9, 363. http://www.biomedcentral.com/1471-2164/9/363

You might also check out GSEA (which can be performed in R).

[seidel]

Holy Cow, the references are all highlighted funny.

[Krzysztof]

Thank you for your answer. I will take a look in these papers.

Answer 2

[Sean Davis]

Take a look at:

http://www.bioconductor.org/packages/release/bioc/html/globaltest.html

Also, just in case you are not aware, you can pull your GEO data into R/bioconductor using:

http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html

Answer 3

[Raygozak]

Search in the bioconductor.org site for tutorials on the affy, lima or marray packages, they should give you a good start. what kind of data do you have (e.g. file format)?

[Krzysztof]

I have just found GSE numbers of datasets in GEO database. I have no experience in R.

Answer 4

[Krzysztof]

As I am not bioinformatician could you suggest any other software/website than R/Bioconductor? It is hard to start form scratch with that software.

Answer 5

[Chris Penkett]

If you don't want to start with BioConductor, and want something with a GUI you could try MeV and/or TM4 or GeneSpring - the latter is commercial and requires a license.