Table 2.
Functional analysis for DE genes at Tpl2-/- 180 mins from different normalization strategies
| Array-level | Strip-level | ||||
|---|---|---|---|---|---|
| Source | Term | Count | FDR | Count | FDR |
| INTERPRO | Four-helical cytokine, core | 4 | 0.94 | 9 | 7.5E-7 |
| SP_PIR_KEYWORDS | cytokine | 5 | 0.21 | 9 | 1.6E-4 |
| KEGG_PATHWAY | Cytokine-cytokine receptor interaction | 5 | 0.84 | 10 | 0.001 |
| KEGG_PATHWAY | Toll-like receptor signaling pathway | - | - | 7 | 0.002 |
| KEGG_PATHWAY | Jak-STAT signaling pathway | 3 | 1.0 | 8 | 0.002 |
| GOTERM_MF_ALL | cytokine activity | 5 | 1.0 | 9 | 0.007 |
| GOTERM_CC_ALL | extracellular region part | 15 | 0.072 | 22 | 0.008 |
| GOTERM_CC_ALL | extracellular space | 14 | 1.0 | 21 | 0.008 |
| GOTERM_CC_ALL | extracellular region | 16 | 0.072 | 23 | 0.013 |
| KEGG_PATHWAY | Regulation of autophagy | - | - | 4 | 0.038 |
| INTERPRO | Interferon alpha | - | - | 4 | 0.039 |
| GOTERM_MF_ALL | receptor binding | 7 | 1.0 | 12 | 0.043 |
| SMART | IFabd | - | - | 4 | 0.043 |
| SP_PIR_KEYWORDS | glycoprotein | 17 | 0.16 | 24 | 0.048 |
| SP_PIR_KEYWORDS | Secreted | 10 | 0.2 | 14 | 0.048 |
The first column is the data source from which terms in the second column come. The third column gives the number of DE genes found by array-level normalization which are associated with the term in the same row in the second column. FDR (False Discovery Rate) from the enrichment test for these genes in all the DE genes found by array-level normalization is given in the fourth column (see METHODS for details). The fifth and sixth column are similar with the third and fourth column respectively except that DE genes examined are from strip-level normalization rather than from array-level normalization.