Question: Enrichment in bacterial core gene
2
gravatar for James Chan
2.3 years ago by
James Chan20
Malaysia
James Chan20 wrote:

Hi, 

I have bacterial genome A and genome B, each with 4,000 and 4,1000 genes. After homologous clustering, I found 1,200 core genes present in both genomes. What I am interested is which GO term is enriched in the core genes of both genome A and B. I am just curious if I am going to calculate manually, using Fisher's exact test in 2x2 contingency table, how am I going to do this? Let say I want to calculate for "Iron transport". For my best understanding in Fisher's exact test, I guess the contingency table should look like this (for genome A):

                      Gene annotated with "Iron transport"       Gene not annotated to "Iron transport"

Core gene                    50                                                              1150

Non core gene             200                                                             2600

 

I don't know is above a correct 2x2 contingency table to find the GO term (by dividing the gene set into core gene VS non core gene), because I saw from other posts, some suggested using whole gene set as background (or core gene VS whole gene set in a genome). I don't know which is the most correct and precise way to do this. I am confused since I am new to statistics and gene enrichment analysis.

I would appreciate if anyone can enlighten me about this question. Thanks in advance.

ADD COMMENTlink written 2.3 years ago by James Chan20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 604 users visited in the last hour