1. Institute for Animal Health Comparative analyses

2. Institute for Animal Health Research at the IAH Infectious diseases of farm animals –Chicken Salmonella Eimeria (coccidiosis) Mareks disease –Cow Foot and Mouth Pestivirus Streptococcal infection (mastitis) –Pig African Swine Fever Foot and Mouth –Sheep TSEs (scrapie) Orbivirus Host-Pathogen Interactions

3. Institute for Animal Health Typical Problem Related species – different phenotype (host- specificity/pathogenicity) Comparative Genomics Gene Expression Analysis Proteomic Analysis

4. Institute for Animal Health Genomics Bacterial –Gene location, structure and function Up to 25,000 misannotated genes by comparative analysis –Pathways, secreted proteins, interaction with host Chicken/Cow –Identification of orthologues and paralogues –Functional annotation poor Eimeria –Unassembled genome –Other related genomes poorly annotated too –Related genomes are largely unspliced, Eimeria is spliced

5. Institute for Animal Health Genomics Comparative genomics –Chicken vs Human Bacterial Kaiser P, Poh T-y, Rothwell L, Avery S, Balu S, Pathania U, Hughes S, Goodchild M, Morrell S, Watson M, Bumstead N, Kaufman J, Young J (2005) A genomic analysis of chicken cytokines and chemokines. J Interferon and Chemokine Research, 25:467–484

6. Institute for Animal Health Current Strategy - Research Comparative genomics –At sequence level, reveals genome organisation Comparative genomics –Also reveals function –Kegg Human: 159 Mouse: 155 Chicken: 31 Cow: 12 –Transfac Human: 1041 Mouse: 765 Chicken: 200 Cow: 10

7. Institute for Animal Health Transcriptomics Overlay gene expression data on functional annotation –GO categories –Pathways –Interactions networks Problem: the relationship of RNA abundance to protein abundance is not straight forward –Post-transcriptional regulation siRNA, miRNA –Post-translational regulation Protein phosphrylation Protein complexes When interpreting gene expression data in terms of the actions of proteins, we must consider models that include all of the above

8. Institute for Animal Health Transcriptomics Salmonella infection Data ExplorationNormalisationDifferential Expression Patterns of Gene Expression

9. Institute for Animal Health Proteomics Mass Spec data –Peptide -> protein -> function? Source of protein search library is often the genome… Lack of functional annotation of genomes of interest Link to microarray data –Through genome –Protein -> peptide -> gene

10. Institute for Animal Health Keywords Genome, proteome, transcriptome Gene, protein, peptide, transcript, promoter, regulator, transcription factor, miRNA, siRNA, enzyme etc Interaction, pathway, network Orthologue, paralogue, homologue Microarray data, sequence data, mass spec data Package, software, method, p-value