Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 estimate the number of copies of the analysed DNA fragments. Bioinformatic and computational analyses Capra hircus genomic sequences longer than 1 kb and including complete coding sequences were retrieved from EMBL database (Sept. 2010). Sequences were clus- tered with BLASTclust http://blast.ncbi.nlm.nih.gov/ on the basis of their identity (> 98%) resulting in 30 sequences covering on the whole 196,665 bp. These sequences were aligned with homologous cattle tran- script regions identified using BLASTN on the basis of the best hits. The global sequence alignment without end-gap penalty was performed with LALIGN program http://www.ch.embnet.org/software/LALIGN_form.html. Exonic regions in goat sequences were defined accord- ing to the cattle annotation of the Btau_4.0 genome ver- sion http://www.ensembl.org/Bos_taurus/Info/Index. The goat CNVRs were mapped on the Btau_4.0 version of the bovine genome. To determine whether goat and cattle CNVRs occur in orthologous regions more often than expected by chance we considered the data reported for cattle in four different experiments [49-52]. The data reported in these four studies were considered separately due to differences in the methods and popu- lations used for CNV detection. A merged list of the CNVRs reported in these investigations was also com- piled (Additional file 4). In one of these cattle studies [48], CNVs were reported with reference to the Btau_3.0 version, therefore the LiftOver tool at the UCSC Genome Bioinformatics Site http://genome.ucsc. edu/cgi-bin/hgLiftOver was used to map CNVs coordi- nates on the Btau_4.0 version. In this case, only 45 out of the reported 79 CNVs were successfully re-mapped. Within each experiment, overlapping CNVs were fused to define CNVRs. These procedures ended up with 37, 368, 177, and 266 CNVRs for Matukumalli et al. [49], Bae et al. [50], Liu et al. [51], and Fadista et al. [52] experiments, respectively, for a total of 764 combined CNVRs (Additional file 4). The number of overlapping segments between each pair of CNVR sets was com- puted and the overlap significance was evaluated with a permutation test [37]. For each experiment, 10,000 arti- ficial random rearrangements of the CNVRs were gener- ated and mapped on the Btau_4.0 bovine genome. The CNVR length distribution was preserved in each random rearrangement. In order to evaluate the significance of the overlap between two CNVR sets, we computed the distribution of the number of overlapping segments between one of the CNVR sets and the 10,000 random rearrangements of the other one. The reported P-value is the fraction of random CNVR rearrangements that obtain at least the same number of overlapping seg- ments as the real one. Page 11 of 15 Goat CNVRs superimposing with cattle transcripts annotated in the Btau_4.0 version were determined on the basis of the genome coordinates, without imposing a minimum overlap threshold. Gene ontology terms associated with bovine transcripts were downloaded with the Ensembl BioMart retrieval system http://www. ensembl.org/biomart/index.html and the complete annotation was obtained by reconstructing the com- plete list of ancestors of each term in the directed acyclic graph described by the OBO file downloaded from the Gene Ontology web site on May 2010 http:// www.geneontology.org/. The GOTermFinder tool was adopted for this task http://search.cpan.org/dist/GO- TermFinder/. We computed the occurrence of each term in the set of transcripts overlapping with goat CNVRs and we compared it with the occurrence of the same term in the whole bovine genome (Btau_4.0 ver- sion). The Fisher exact test was adopted to assess the significance of the overrepresentation of the terms in the set of transcripts overlapping with the goat CNVRs. The multiple-hypothesis correction [93] was adopted for discriminating the significant terms at dif- ferent False Discovery Rates (FDR): 0.001, 0.01, 0.05, and 0.1. To supplement the functional annotation, PANTHER Molecular Function terms were assigned to all bovine transcripts using the Hidden Markov Model scoring tools of the PANTHER (Protein ANalysis THrough Evo- lutionary Relationships) Classification System version 6.1 http://panther6.ai.sri.com/tools/hmmScoreForm.jsp. Similarly to the GO annotation, the distribution of the PANTHER terms in the set of transcripts overlapping with goat CNVRs was compared with the occurrence in the whole genome and the significance of the overrepre- sentation was evaluated with the Fisher exact test adopt- ing the multiple-hypothesis correction. aCGH data have been submitted to the gene expres- sion omnibus http://www.ncbi.nlm.nih.gov/geo/ under the accession number GSE24436. Additional material Additional file 1: List of CNVs identified in the analysed goats. The Excel file reports the chromosome, the nucleotides position of the CNV start and end (referred to the Btau_4.0 genome assembly), the size of the CNV in bp, the number of valid probes in the CNV (additional probes are included in CNV considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNV), log2 mean of the probes in the CNV (see Methods), the type of CNV (gain/loss), the goat sample (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen; numbers after the breed symbols indicate the different animals used in the aCGH experiment), and the goat breed. Additional file 2: List of CNVRs obtained by merging overlapping CNVs across animals. The Excel file reports the progressive CNVR number, the chromosome, the nucleotides position of the CNVR start and end (referred to the Btau_4.0 genome assembly), the size of the