Hi,

Did you check the manual: http://bioinfo.cau.edu.cn/agriGO/manual.php

The graphical result is a GO hieratical image containing all statistically significant terms. These nodes in the image are classified into ten levels which are associated with corresponding specific colors. The smaller of the term's adjusted p-value, the more significant statistically, and the node's color is darker and redder (Note: adjusted p-value here means that the value of the multiple-test adjusted p-value). Inside the box of the significant terms, the information includes: GO term, adjusted p-value, GO description, item number mapping the GO in the query list and background, and total number of query list and background. But when those term whose adjusted p-value is higher than the cutoff set by the user, only GO information will be given in the box. To better understand the graphical result, investigation of the annotation diagram is suggested.

António