how to arrange data for pathway analysis ?

Question

[Learner]

Hello ,

I have two tricky questions and I appreciate any useful comment

1- I have 6 samples , 3 control (two of them are biological replicate) and 3 treated (two of them are biological replicate). How should I use them for pathway analysis ? for example does it make sense to do like this ?

Average the three control (A) , average the three treated replicate (B), then B/A ==> fold change is this right?

1- which pathway analysis is giving the statistical differences for a pathway, for example with IPA , you can say is a pathway significantly expressed by a set of genes or not based on p-value and z but is there any other pathway analazor which gives such results ?

Thanks

Answer 1

[Ron]

Hi,

Yes,the fold change B/A is correct. Use log2fold change of all genes to do pathway analysis. You can use GSEA from Broad institute for this.

Answer 2

[igor]

If you would like to try other pathway analysis tools, check these previous threads for many alternatives:

• Is There A Free Alternative To Ingenuity Pathway Analysis?
• Mapping Genes To Pathway