I have 34727 genes in my gene universe. From those only 19622 have at least one GO term attached. Also there is list of genes of interest with 467 genes, out of them only 80 have GO annotation. From those data i created three topGOdata objects: one for terms related to biological process, another one related to molecular function ant the third one for GO terms associated with cellular component category. In the summary i see:
> myGOdata_BP
------------------------- topGOdata object -------------------------
Ontology:
- BP
34727 available genes (all genes from the array):
- 467 significant genes.
1810 feasible genes (genes that can be used in the analysis):
- 2 significant genes.
GO graph (nodes with at least 1 genes):
- a graph with directed edges
- number of nodes = 646
- number of edges = 1369
------------------------- topGOdata object -------------------------
> myGOdata_CC
------------------------- topGOdata object -------------------------
Ontology:
- CC
34727 available genes (all genes from the array):
- 467 significant genes.
1288 feasible genes (genes that can be used in the analysis):
- 0 significant genes.
GO graph (nodes with at least 1 genes):
- a graph with directed edges
- number of nodes = 164
- number of edges = 328
------------------------- topGOdata object -------------------------
> myGOdata_MF
------------------------- topGOdata object -------------------------
Ontology:
- MF
34727 available genes (all genes from the array):
- 467 significant genes.
3658 feasible genes (genes that can be used in the analysis):
- 2 significant genes.
GO graph (nodes with at least 1 genes):
- a graph with directed edges
- number of nodes = 928
- number of edges = 1164
------------------------- topGOdata object -------------------------
So, i can not understand why (even i'll make a summation of gene amount from all three objects) i have a such tiny amount of feasible genes and significant (genes of interest) ones in my analysis? How i can figure out it?
