Table 1.
The output of GOATOOLS GO grouping is a list.
| A) Ungrouped GO IDs sorted by P-value | ||
|---|---|---|
| GO Name | P-value | |
| immune system process | 3.74E-07 | |
| defense response to protozoan | 5.56E-06 | |
| defense response to virus | 2.93E-04 | |
| positive regulation of extrinsic apoptotic signaling pathway | 5.94E-04 | |
| positive regulation of T cell mediated cytotoxicity | 7.30E-04 | |
| response to bacterium | 7.30E-04 | |
| +reg. of cysteine-type endopeptidase activity in apoptotic process | 1.35E-02 | |
| pyroptosis | 1.86E-02 | |
| positive regulation of I-kappaB kinase/NF-kappaB signaling | 3.15E-02 | |
| +reg. of tumor necrosis factor-mediated signaling pathway | 3.70E-02 | |
| antigen processing and presentation of exogenous antigen | 4.32E-02 | |
| purinergic nucleotide receptor signaling pathway | 4.32E-02 | |
| B) Grouped GO IDs sorted by P-value | ||
| GO Name | P-value | Section |
| positive regulation of extrinsic apoptotic signaling pathway | 5.94E-04 | cell death |
| +reg. of cysteine-type endopeptidase activity in apoptotic process | 1.35E-02 | cell death |
| pyroptosis | 1.86E-02 | cell death |
| mmune system process | 3.74E-07 | immune |
| positive regulation of T cell mediated cytotoxicity | 7.30E-04 | immune |
| antigen processing and presentation of exogenous antigen | 4.32E-02 | immune |
| positive regulation of I-kappaB kinase/NF-kappaB signaling | 3.15E-02 | signaling |
| +reg. of tumor necrosis factor-mediated signaling pathway | 3.70E-02 | signaling |
| purinergic nucleotide receptor signaling pathway | 4.32E-02 | signaling |
| defense response to protozoan | 5.56E-06 | viral/bacteria |
| defense response to virus | 2.93E-04 | viral/bacteria |
| response to bacterium | 7.30E-04 | viral/bacteria |
GOATOOLS grouping makes GO lists easier to read. Even a short list of GO terms can be hard to to read and difficult to discern which GO terms might be related (A). GOATOOLS grouping makes results easier to read (B). GO terms in Table A are sorted by P-value. In Table B, GO terms are grouped first and then sorted by P-value. These tables were produced using GOATOOLS grouping and table writing code. The first column, ‘GO Name’ is the name of the GO term found in the GO DAG. The second column shows the P-value obtained from running a GOEA analysis. The third column shows the functional group containing the GO term, called a ‘section name’. Normally GO grouping lists are black and white, but a table can be colorized (shown) if provided with a Python dictionary where the key is the section and the value is the color. The creation of section names for grouping is described in detail in the text.