Institute for Animal Health Institute for Animal Health Comparative analyses
Mar 28, 2015
Institute for Animal Health
Institute for Animal Health
Comparative analyses
Institute for Animal Health
Research at the IAH
• Infectious diseases of farm animals– Chicken
• Salmonella• Eimeria (coccidiosis)• Marek’s disease
– Cow• Foot and Mouth• Pestivirus• Streptococcal infection (mastitis)
– Pig
• African Swine Fever• Foot and Mouth
– Sheep• TSEs (scrapie)• Orbivirus
Host-Pathogen Interactions
Institute for Animal Health
Typical Problem
Related species – different phenotype (host-
specificity/pathogenicity)
Comparative Genomics
Gene Expression Analysis
Proteomic Analysis
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
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
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
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
Institute for Animal Health
Transcriptomics
• Salmonella infection
Data Exploration Normalisation Differential Expression
Patterns of Gene Expression
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
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