BMC Genomics 2006, 7:42 http://www.biomedcentral.com/1471-2164/7/42 expressed genes and all RefSeq genes on the array were subsequently screened for the presence of all unique motifs using MAST. Once again, reverse complement ori- entation of the motifs was allowed and the results obtained were analysed using Fisher's exact test based on the number of RefSeq promoters with a combined motif significance of P < 0.0001 in each of the groups. Authors' contributions OMK extracted all RNA, carried out the microarray exper- iments, Northern blotting and Gene Ontology analysis as well as preparing the manuscript. AZ carried out the MEME and MAST analysis. TW and DLH designed, con- structed and validated the ovine cDNA arrays. GJG was responsible for all animal care, handling and experimen- tation. DBB developed the microarray normalisation pro- cedure and carried out statistical analysis, AFM curated the EST database, assembled the contigs and provided bioin- formatics support. AMC and JCM conceived the study, participated it its design, coordination, analysis and writ- ing. All authors read and approved the final manuscript. Additional material Additional File 1 This file contains all motifs detected by MEME in the promoter regions of genes more highly expressed in susceptible animals. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-42-S1.pdf] Additional File 2 This file contains all motifs detected by MEME in the promoter regions of genes more highly expressed in resistant animals. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-42-S2.pdf] Additional File 3 This file ranks the ESTs on the array according to their differential expres- sion and contains statistical information for each EST on the array. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-42-S3.xls] Acknowledgements We thank Roger Wheeler, Wendy Bain, Chris Morris, Kevin Knowler, Mary Wheeler and Nadia McLean for assistance with maintenance of the Perendale selection lines, animal handling and slaughter. This work was funded by the Ovita Consortium Ltd. References 1. Dominik S: Quantitative trait loci for internal nematode resistance in sheep: a review. Genet Sel Evol 2005, 37 Suppl 1:S83-96. 2. Balic A, Bowles VM, Meeusen EN: The immunobiology of gas- trointestinal nematode infections in ruminants. Adv Parasitol 2000, 45:181-241. 3. Gill HS: Genetic control of acquired resistance to haemon- chosis in Merino lambs. Parasite Immunol 1991, 13(6):617-628. 4. 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