Table 7 Functional analysis for DE genes at Tpl2-/- 180 mins obtained from different normalization strategies when probe filtering is applied
From: Illumina WG-6 BeadChip strips should be normalized separately
| Â | Â | Array-level | Strip-level | ||
|---|---|---|---|---|---|
Source | Term | Count | FDR | Count | FDR |
INTERPRO | Four-helical cytokine, core | 7 | 1.7E-4 | 9 | 2.0E-6 |
SP_PIR_KEYWORDS | cytokine | 8 | 2.9E-4 | 10 | 3.7E-5 |
KEGG_PATHWAY | Cytokine-cytokine receptor interaction | 8 | 0.019 | 11 | 2.8E-4 |
KEGG_PATHWAY | Toll-like receptor signaling pathway | 6 | 0.01 | 9 | 5.3E-5 |
KEGG_PATHWAY | Jak-STAT signaling pathway | 6 | 0.054 | 9 | 5.7E-4 |
GOTERM_MF_ALL | cytokine activity | 8 | 9.9E-3 | 10 | 1.1E-3 |
GOTERM_CC_ALL | extracellular region part | 19 | 3.2E-3 | 24 | 5.6E-3 |
GOTERM_CC_ALL | extracellular space | 18 | 4.1E-3 | 23 | 4.8E-3 |
GOTERM_CC_ALL | extracellular region | 20 | 3.7E-3 | 25 | 0.01 |
KEGG_PATHWAY | Regulation of autophagy | 3 | 0.4 | 5 | 2.8E-3 |
INTERPRO | Interferon alpha | 3 | 0.81 | 4 | 0.037 |
GOTERM_MF_ALL | receptor binding | 10 | 0.1 | 13 | 0.016 |
SMART | IFabd | 3 | 0.57 | 5 | 1.2E-3 |
SP_PIR_KEYWORDS | glycoprotein | 20 | 0.021 | 24 | 0.23 |
SP_PIR_KEYWORDS | Secreted | 13 | 0.017 | 14 | 0.21 |
GOTERM_BP_ALL | response to other organism | 6 | 0.24 | 8 | 0.013 |
SP_PIR_KEYWORDS | antiviral defense | 3 | 0.38 | 5 | 4.1E-3 |