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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

   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