Institute for Animal Health Comparative analyses.

Institute for Animal Health


Comparative analyses


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


Typical Problem

Related species – different phenotype (host-

specificity/pathogenicity)

Comparative Genomics

Gene Expression Analysis

Proteomic Analysis


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


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


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


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


Transcriptomics

• Salmonella infection

Data Exploration Normalisation Differential Expression

Patterns of Gene Expression


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


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

Institute for Animal Health Comparative analyses.

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