Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 Page 9 of 15 Table 4 Gene ontology (GO) categories significantly overrepresented (FDR, P<0.001) in goat CNVRs GO level Molecular Function GO term Go name GO:0005525 GTP binding No. in goat CNVRs Expected no. Biological processes Cellular components GO:0032561 guanyl ribonucleotide binding GO:0003924 GTPase activity GO:0019001 guanyl nucleotide binding GO:0017111 nucleoside-triphosphatase activity GO:0016462 pyrophosphatase activity GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides GO:0016817 hydrolase activity, acting on acid anhydrides GO:0015171 amino acid transmembrane transporter activity GO:0004869 cysteine-type endopeptidase inhibitor activity GO:0017076 purine nucleotide binding GO:0046943 carboxylic acid transmembrane transporter activity GO:0005342 organic acid transmembrane transporter activity GO:0042974 retinoic acid receptor binding GO:0046965 retinoid X receptor binding GO:0022804 active transmembrane transporter activity GO:0032553 ribonucleotide binding GO:0032555 purine ribonucleotide binding GO:0005275 amine transmembrane transporter activity GO:0050896 response to stimulus GO:0006952 defense response GO:0006950 response to stress GO:0051704 multi-organism process GO:0046942 carboxylic acid transport GO:0015849 organic acid transport GO:0051707 response to other organism GO:0009617 response to bacterium GO:0042742 defense response to bacterium GO:0042613 MHC class II protein complex GO:0042611 MHC protein complex 24 24 16 24 25 25 25 25 6 5 37 6 6 3 3 12 37 37 6 41 16 25 13 8 8 10 9 7 5 7 3.7 3.8 2.1 3.9 8.4 8.6 8.6 8.8 0.50 0.37 19 0.73 0.74 0.094 0.094 3.3 18 18 0.55 15 2.6 8.0 2.2 0.76 0.77 1.5 1.1 0.68 0.14 0.62 The complete list of overrepresented GO and PANTHER categories is reported in Additional file 10 and Additional file 11, respectively, including details about the categories of the whole cattle genome (Btau_4.0 version) used as reference. Methods Array CGH We analysed CNVs in the goat genome by means of a cross-species aCGH experiment using the Roche Nim- bleGen platform (Roche NimbleGen Inc., Madison, WI; http://www.nimblegen.com) based on custom tiling arrays designed on the bovine (Bos taurus) genome, Btau_4.0 version [74], including a fraction of BTA13 of the University of Maryland (UMD) Bos taurus v. 2.0 assembly (ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/ Bos_taurus_UMD_2.0/[75]). Arrays contained ~385,000 probes on a single slide to provide an evenly distributed coverage with an average interval of ~6 kb for the Btau_4.0 genome. The BTA13 of the UMD v. 2.0 assem- bly was included from nucleotide position 48 M bp to nucleotide position 78 M bp (4,673 oligonucleotides and average spacing of ~6 kb). This chromosome region was analysed as internal control because it contains the ASIP gene, not assembled in the BTA13 of the Btau_4.0 ver- sion. We previously showed that this goat gene is included in a CNVRs in different goat breeds [22]. Goat genomic DNA was extracted from blood of 2 Camosciata delle Alpi, 3 Girgentana, 3 Saanen, 1 black and 1 brown Murciano-Granadina goats using the Wizard® Genomic DNA Purification kit (Promega Cor- poration, Madison, WI). All analysed animals were females. Reference DNA sample of one Camosciata delle Alpi goat (C1) was labeled with Cy5 and co-hybridised with the other test DNA samples labeled with Cy3 on 9 different arrays. A self hybridisation (reference labeled