Open Access Highly Accessed Research article

Structural and functional annotation of the porcine immunome

Harry D Dawson1, Jane E Loveland2, Géraldine Pascal3, James GR Gilbert2, Hirohide Uenishi4, Katherine M Mann5, Yongming Sang6, Jie Zhang7, Denise Carvalho-Silva152, Toby Hunt2, Matthew Hardy2, Zhiliang Hu8, Shu-Hong Zhao7, Anna Anselmo9, Hiroki Shinkai4, Celine Chen1, Bouabid Badaoui9, Daniel Berman5, Clara Amid152, Mike Kay2, David Lloyd2, Catherine Snow2, Takeya Morozumi10, Ryan Pei-Yen Cheng8, Megan Bystrom8, Ronan Kapetanovic11, John C Schwartz12, Ranjit Kataria13, Matthew Astley2, Eric Fritz8, Charles Steward2, Mark Thomas2, Laurens Wilming2, Daisuke Toki10, Alan L Archibald11, Bertrand Bed’Hom14, Dario Beraldi11, Ting-Hua Huang8, Tahar Ait-Ali11, Frank Blecha6, Sara Botti9, Tom C Freeman11, Elisabetta Giuffra149, David A Hume11, Joan K Lunney5, Michael P Murtaugh12, James M Reecy8, Jennifer L Harrow2, Claire Rogel-Gaillard14* and Christopher K Tuggle8*

Author Affiliations

1 USDA-ARS, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, MD 20705, USA

2 Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK

3 INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France

4 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

5 USDA ARS BA Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA

6 Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA

7 Laboratory of Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Wuhan 430070, PR China

8 Department of Animal Science, Iowa State University, Ames, IA 50011, USA

9 Parco Tecnologico Padano, Integrative Biology Unit, via A. Einstein, 26900, Lodi, Italy

10 Institute of Japan Association for Technology in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan

11 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK

12 Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA

13 National Bureau of Animal Genetic Resources, P.B. 129, GT Road By-Pass, Karnal 132001, (Haryana), India

14 INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350, Jouy-en-Josas, France

15 Current affiliation: EMBL Outstation-Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambs CB10 1SD, UK

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BMC Genomics 2013, 14:332  doi:10.1186/1471-2164-14-332

Published: 15 May 2013

Additional files

Additional file 1: Table S1:

Pig-human-mouse-bovine gene family comparisons.

Format: XLSX Size: 116KB Download file

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Additional file 2: Table S2:

Known gene sequences that are missing from Build 10.2.

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Additional file 3: Table S3:

True duplicated genes in Build 10.2.

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Additional file 4: Table S4:

Artifactually duplicated genes in Build 10.2.

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Additional file 5: Table S5:

List of datasets used in immune response clustering analysis.

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Additional file 6: Table S6:

Gene Ontology annotation of Biolayout Express3D clusters from immune response network shown in Figure 2.

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Additional file 7: Table S7:

Summary of annotations of selected clusters from immune response clustering analysis.

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Additional file 8: Figure S1:

Expression pattern of MCL cluster 17 shows gene activation after immune stimulation/infection in specific experimental datasets. In blue is shown the average expression of the 81 probesets in cluster 17. Details on each dataset are shown below the graph; some example patterns are highlighted in red. See abbreviations in legend to Figure 3.

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Additional file 9: Figure S2:

Expression pattern of MCL cluster 26 shows gene expression common to Lymph Node and blood datasets without a strong pattern related to immune stimulation. In brown is shown the average expression of the 48 probesets in cluster 26. Details on each dataset are shown below the graph. See abbreviations in legend to Figure 3.

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Additional file 10: Figure S3:

Expression pattern of MCL cluster 48 shows gene activation after immune stimulation/infection in many experimental datasets. In orange is shown the average expression of the 24 probesets in cluster 26. Details on each dataset are shown below the graph; some example patterns are highlighted in red. See abbreviations in legend to Figure 3.

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Additional file 11: Table S8.:

Results of positive selection computation on the 242 pig proteins from MCL cluster 4.

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Additional file 12: Figure S4.:

Results of positive selection calculation are visualized on primary sequence of (A) PPP2R5C, (B) GBP1, (C) HEXB and (D) CASP8 pig proteins. Amino acids in green font are under purifying selection. Amino acids in orange and red font are under positive selection with posterior probabilities greater than 95% or 99%, respectively. Amino acids in white font target those for which no information is available (no calculation was performed by PAML due to at least one gap in the multiple sequence alignment at this position). Amino acids are in grey font where results are not significant enough to infer either purifying or positive selection. Protein domains, as predicted by InterPro resources (see Methods) are represented by colored bars under amino acid sequences.

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