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Table 2 Functional analysis for DE genes at Tpl2-/- 180 mins from different normalization strategies

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 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
  1. 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.