Comparative Transcriptome and DNA methylation analyses of ...
Institute for Animal Health Comparative analyses.
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Transcript of Institute for Animal Health Comparative analyses.
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Institute for Animal Health
Institute for Animal Health
Comparative analyses
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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
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Institute for Animal Health
Typical Problem
Related species – different phenotype (host-
specificity/pathogenicity)
Comparative Genomics
Gene Expression Analysis
Proteomic Analysis
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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
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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
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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
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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
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Institute for Animal Health
Transcriptomics
• Salmonella infection
Data Exploration Normalisation Differential Expression
Patterns of Gene Expression
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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
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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