Table 4.
Immune response functional analysis discriminating stage 4S (n=12) from [1yr−] stage 4 (n=8) according to S.B.I.M.E. tool
| Ng | Ngc | Ns | % | Z | P | Genes | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BioCarta | ||||||||||||||||||||
| Ras‐independent pathway in NK cell‐mediated cytotoxicity | 17 | 17 | 4 | 23.5 | 4.84 | 1.32E‐06 | PTPN6 | ⇓ | SYK | ⇓ | LAT | ⇓ | KLRC1 | ⇓ | ||||||
| T cytotoxic cell surface molecules | 12 | 10 | 2 | 20 | 3.25 | 1.14E‐03 | CD28 | ⇓ | THY1 | ⇓ | ||||||||||
| E2F1 destruction pathway | 9 | 9 | 2 | 22.2 | 3.24 | 1.20E‐03 | SKP2 | ⇑ | CUL1 | ⇑ | ||||||||||
| T helper cell surface molecules | 12 | 10 | 2 | 20 | 3.15 | 1.63E‐03 | CD28 | ⇓ | THY1 | ⇓ | ||||||||||
| Role of Tob in T cell activation | 15 | 12 | 2 | 16.7 | 3.1 | 1.91E‐03 | IFNG | ⇓ | CD28 | ⇓ | ||||||||||
| Gene ontology – biological process | ||||||||||||||||||||
| Defense response | 98 | 77 | 7 | 9.1 | 3.13 | 1.73E‐03 | IFNG | ⇓ | MX2 | ⇓ | IFNA21 | FLJ10979 | ⇑ | PTPRCAP | ⇓ | CD84 | ⇓ | SP140 | ⇓ | |
| Humoral immune response | 28 | 25 | 3 | 12 | 2.7 | 6.86E‐03 | CD28 | ⇓ | BRDG1 | ⇓ | LTF | ⇓ | ||||||||
| Integrin‐mediated signaling pathway | 45 | 39 | 4 | 10.3 | 2.61 | 9.03E‐03 | ITGB7 | ⇓ | ITGA7 | ⇓ | ITGB3 | ⇓ | SYK | ⇓ | ||||||
| Gene ontology – molecular function | ||||||||||||||||||||
| MHC class I receptor activity | 13 | 11 | 2 | 18.2 | 2.85 | 4.36E‐03 | KLRF1 | ⇓ | ULBP3 | ⇑ | ||||||||||
| 4s<[1yr−] stage 4 | ⇓ | |||||||||||||||||||
| 4s>[1yr−] stage 4 | ⇑ | |||||||||||||||||||
Using ANOVA, only functional categories with a p‐value <0.01 were selected according to the Z‐score (comparison of the observed percentage to a randomized set of theoretical percentages). Each row corresponds to a category found by S.B.I.M.E.Kauffmann et al. (2008), ordered by increasing p‐value. “Ng”=genes number in the functional category. “Ngc”=genes number present in the data set. “Ngc”>“Ng” if there are several oligonucleotides for the same gene on the array. “Ns”=number of significantly differentially expressed genes. “%” is the percentage of genes significantly expressed (Ns/Ngc*100). “P”=p‐value associated to the Z‐score calculation, i.e., the probability to find this functional category significant by chance. Following this column, the S.B.I.M.E. output file normally presents all the genes (not shown).