Hi! I am using Blast2go and it seems very useful, however, I don't understand the results I am getting from the GO graphs. I uploaded two Interproscan files: (1) about protein-coding genes candidates, (2) effector Candidates. Both files are from the same organism. The only difference is that for file (2) I used Signalp and Effectorp to detect effector candidates and then I used the Interproscan command line.
Now, when I plot the GO terms, the graphics are the same for file (1) and (2), even though the number of GO terms vary significantly.
For file (1): Total protein-coding genes = 11.874; Goterms = 6.198
For file (2): Effector proteins = 128; Goterms = 36
So my question is why am I having the exact GO graphs, for molecular and biological processes, if the GO terms vary in number for each file.
Thank you in advance for your help.