Open Access Research article

Comparison and contrast of genes and biological pathways responding to Marek’s disease virus infection using allele-specific expression and differential expression in broiler and layer chickens

Sudeep Perumbakkam1, William M Muir1, Alexis Black-Pyrkosz2, Ron Okimoto3 and Hans H Cheng2*

Author Affiliations

1 Department of Animal Science, Purdue University, West Lafayette, IN, 47907, USA

2 Avian Diseases and Oncology Laboratory, USDA, ARS, East Lansing, MI, 48823, USA

3 Cobb-Vantress, Siloam Springs, AR, 72761, USA

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BMC Genomics 2013, 14:64  doi:10.1186/1471-2164-14-64

Published: 30 January 2013

Additional files

Additional file 1:

Table S1.Broiler raw reads, alignment, and raw SNPs. Table S2. Layer raw reads, alignment, and raw SNPs. Table S3. List of ASE SNPs in broiler samples (p<0.05) in response to MDV infection. Table S4. List of ASE SNPs in layer samples (p<0.05) in response to MDV infection. Table S5. Common SNPs between broilers and layer ASE samples in response to MDV infection. Table S6. ANNOVAR classification of broiler SNPs based on function. Table S7. ANNOVAR classification of layer SNPs based on function. Table S8. Genes differentially expressed (P<0.05) following MDV infection in broilers. Table S9. Genes differentially expressed (P<0.05) following MDV infection in layers. Table S10. Functional annotatiion clustering of ASE genes in response to MDV in broilers using DAVID. Table S11. Functional annotatiion clustering of ASE genes in response to MDV infection in layers using DAVID. Table S12. Functional annotatiion clustering of nonsynonymous genes in response to MDV infection in broilers using DAVID. Table S13. Functional annotatiion clustering of nonsynonymous genes in response to MDV infection in layers using DAVID. Table S14. Common nonsynonymous genes between broilers and layers. Table S15. Functional annotation of 14 common nonsynonymous genes between broilers and layers. Table S16. Functional annotatiion clustering of DE genes in response to MDV infection in broilers using DAVID. Table S17. Functional annotatiion clustering of DE genes in response to MDV infection in layers using DAVID.

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Additional file 2:

Figure S1Distribution of SNPs exhibiting ASE in response to MDV infection in chicken chromosomes.

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