Hello

I am using go-seq for gene enrichment study. I am having few confusion I will be very grateful if I can get some help.

1) I know we need gene length to calculate the bias.

2) I want to do gene enrichment of two groups compared to the control group.

• i got a list of transcripts which are commonly differential expressed in both theses group(A, B) against the control group.

• Now, I need to do gene enrichment of these genes (that are commonly differential in both groups against the control group).

• For this I need to feed the gene names and element values 0 if the gene is not differentially expressed or 1 if the gene is differentially expressed.

• I entered the element value for all the common genes that were differentially expressed in both the group (against control) as 1 while for other genes as 0.

My question is there are other gene where I kept element value as 0, but they are differentially expressed in a single group(lets say in A) . Hope I m not doing something wrong, as My interest is to do gene enrichment of genes that are differently expressed in both group against control.

Thanking you in advance for your help.

1. You should use the length that matches how you counted reads. The length should be the total length of the annotation that you input to the read counting software for that transcript ID.

2. There is no problem doing an GO analysis for reads up-regulated in both groups. You can choose any set of genes that makes biological sense to you.