BMC Genomics 2006, 7:42 http://www.biomedcentral.com/1471-2164/7/42 Table 2: Genes more highly expressed in the duodenum of genetically resistant animals compared to susceptible Human RefSeq: Genbank accession number Gene description NM_003789 TNFRSF1A-associated via death domain NM_000988 Ribosomal protein L27 NM_007209 Ribosomal protein L35 NM_014716 Centaurin, beta 1 NM_000477 Albumin NM_175571 IMAP family member 8, GTPase NM_006118 HS1 binding protein NM_005801 Putative translation initiation factor NM_182752 Family with sequence similarity 79, member A NM_006827 Transmembrane trafficking protein NM_001107 Erythrocyte acylphosphatase 1 NM_000211 Integrin, beta 2 NM_000613 Hemopexin NM_145869 Annexin A11 NM_002872 Small GTP binding rho family protein NM_033657 Death associated protein 3 implying that it may be involved in the healing response following injury [28]. When measured by Northern blot, SPINK1 expression was increased two fold in the suscepti- ble animals compared to the resistant animals (Figure 2B) and this increased expression was highly significant (P = 0.005). In particular two of the resistant animals had very low levels of SPINK1 expression although expression in the other two resistant animals was still lower than expres- sion in any of the susceptible animals. Differential expression of the immunity associated GTPase, GIMAP8, was also confirmed. This gene is a mem- ber of a novel family of GTPases conserved among higher plants and vertebrates [29]. Human GIMAP proteins are known to be expressed most highly in the spleen and lymph nodes, but expression has also been detected in the digestive tract [30]. GIMAP proteins are thought to be involved in the control of cell survival and response to infection and GIMAP8 has been shown to have anti-apop- totic functions. Expression of this gene is known to be decreased in the spleen of mice infected with the proto- zoan parasite Plasmodium chabaudi [29]. GIMAP8 was expressed 2.6 fold more highly in the intestine of resistant animals compared to susceptible (Figure 2C) as measured by Northern blot. This differential expression is also highly significant (P = 0.0018). It is notable that the fold increase in expression of both GIMAP8 and SPINK1 is markedly higher when quantitated by Northern blot rather than when quantitated by microarray. Differential transcript expression of GIMAP8 was also observed with the four resistant animals predominantly expressing an approximately 3,300 bp transcript, although a larger tran- Gene name TRADD RPL27 RPL35 CENTB1 ALB GIMAP8 HAX1 SUI1 FAM79A TMP21 ACYP1 ITGB2 HPX ANXA11 RAC2 DAP3 Ensembl human gene cytogenetic band 16q22.1 17q21.31 9q33.3 17p13.1 4q13.3 7q36.1 1q21.3 17q21.2 1p36.32 14q24.3 14q24.3 21q22.3 11p15.4 10q22.3 22q13.1 1q22 Contig BLAST E value 1 × 10-136 4 × 10-98 1 × 10-141 7 × 10-62 1 × 10-151 2 × 10-22 0 0 1 × 10-117 4 × 10-19 1 × 10-114 0 1 × 10-121 1 × 10-122 0 0 Fold increase in expression 1.3 1.2 1.2 1.3 1.2 1.2 1.2 1.1 1.2 1.1 1.2 1.2 1.2 1.2 1.2 1.1 P value 2.9 × 10-8 5.9 × 10-7 2.4 × 10-6 2.9 × 10-6 3.4 × 10-6 4.2 × 10-6 4.6 × 10-6 4.7 × 10-6 5.3 × 10-6 7.7 × 10-6 9.2 × 10-6 1 × 10-5 1.5 × 10-5 2 × 10-5 2 × 10-5 2.5 × 10-5 script of approximately 4,100 bp could still be detected. In contrast three of the susceptible animals predominantly expressed the larger transcript although the smaller tran- script was detectable, while one susceptible animal expressed the smaller transcript. The precise size of the GIMAP8 transcript is unknown in sheep. Transcript vari- ants of this gene, with sizes of 4,700 bp and 4,200 bp, have been previously reported in human and transcript variants of size 4,200 bp and 2,900 bp have been reported in mouse [29,30]. Gene Ontology (GO) terms significantly associated with the differentially expressed genes were found using EASEonline [31] and are listed in Table 3. A number of GO terms were significantly associated (P < 0.05) with the genes more highly expressed in the intestine of susceptible animals. These terms pertain to an organism's response to stress and stimulus and imply that despite the absence of nematodes from the environment of the susceptible ani- mals, their gastrointestinal tract is still responding to insults or injuries, possibly by other pathogens. The only GO term significantly associated with genes more highly expressed in resistant animals was "cellular process" indi- cating that the intestine of these animals does not appear to be under stress. Promoter regions of the 16 genes more highly expressed in resistant animals and the 25 genes more highly expressed in susceptible animals were analysed for com- mon cis-regulatory motifs. The analysis was performed using the MEME motif prediction program [32]. Only two motifs were significant and both were found in the pro- Page 4 of 12 (page number not for citation purposes)