BMC Genomics 2009, 10:150 http://www.biomedcentral.com/1471-2164/10/150 Table 1: Numbers of probes and corresponding unique genes in different conditions Condition Present on Mouse Ref-8 Detected (in at least one out of four conditions) Surgery: overall effect Surgery: effect in C57BL/6J Surgery: effect in C57.YA Strain: overall effect Strain: effect in CX Strain: effect in sham (intact) Interaction between surgery and strain Probes Corresponding unique genes 25,697 12,764 3,030 1,103 2,706 3,282 3,209 479 318 18,118 8,297 2,274 845 2,042 2,508 2,421 381 249 effect of CX varied according to the origin of chrY, we per- formed post-hoc analyses on the hybridization results obtained with probes from all interaction genes. Accord- ingly, we found that the expression of interaction genes was differentially affected by strain to a greater extent in CX (177/249 genes) than in intact sham (99/249 genes) mice (with 3 genes where the effect of surgery treatment did not reach significance with the post-hoc analysis) (Fig- ure 4). Likewise, genes responded to CX in a strain-specific manner to a greater extent in C57.YA (204/249 genes) than in C57BL6/J (77 genes/249) mice (with also 3 genes where the effect of strain did not reach significance with the post-hoc analysis) (Figure 4). In order to assess the biological significance of the interac- tion genes, we performed a Set Enrichment Test for every pathway in the Kyoto Encyclopedia of Genes and Genomes (KEGG) [14] to calculate the probability of observing a given number of selected genes in a pathway by chance. The six following KEGG pathways showed enrichment for interaction genes using a p-value ≤ 0.05 as a criteria for selection: circadian rhythm [containing Arntl1 (also known as Bmal1), Per2, Per3 and Cry2], p53 signaling pathway (containing Cdkn1a, Gadd45g, Ccnd1 and Pten), melanoma (also containing Cdkn1a, Ccnd1 and Pten, as well as Fgf7), cytokine-cytokine receptor interaction (contain- ing Acvr2b, Ccl8, Tnfrsf12a, Cxcl1 and IL28ra), leukocyte sFVteirgnauinnrsdeiua4sgerdamins tshheowcuinrrgetnhtesdtuisdtyrib(nut=io4n poefr"ignrtoeurapc)tion genes" within the 2 particular surgery groups or within the 2 particular Venn diagrams showing the distribution of "interaction genes" within the 2 particular surgery groups or within the 2 particular strains used in the current study (n = 4 per group). Page 4 of 11 (page number not for citation purposes)