Open Access Highly Accessed Research article

Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems

Jason E McDermott1, Harish Shankaran1, Amie J Eisfeld2, Sarah E Belisle3, Gabriele Neuman2, Chengjun Li2, Shannon McWeeney45, Carol Sabourin6, Yoshihiro Kawaoka2789, Michael G Katze103 and Katrina M Waters1*

Author Affiliations

1 Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, Washington, USA

2 Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA

3 Department of Microbiology, University of Washington, Seattle, Washington, USA

4 Oregon Health and Science University, Division of Biostatistics, Department of Public Health and Preventive Medicine, Portland, Oregon, USA

5 Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon, USA

6 Battelle, Columbus, Ohio, USA

7 Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan

8 Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, 108-8639, Japan

9 ERATO Infection-Induced Host Responses Project, Saitama 332-0012, Japan

10 Washington National Primate Research Center, University of Washington, Seattle, Washington, USA

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BMC Systems Biology 2011, 5:190  doi:10.1186/1752-0509-5-190

Published: 11 November 2011

Additional files

Additional file 1:

Supplemental information; Supplemental methods and results for the manuscript.

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Additional file 2:

Table S1; Cross-coexpression analysis of mouse, macaque and human Calu-3 cell response to influenza infection.

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Additional file 3:

Table S2; Supplemental table showing transcripts with conserved dynamics in Calu-3 cells, mouse and macaque responding to VN1203 infection.

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Additional file 4:

Table S3; Supplemental table showing cluster membership of the 10 cluster model with macaque information.

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Additional file 5:

Table S4; Numbers of genes and mouse or macaque homologs differentially expressed in each cluster.

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Additional file 6:

Hierarchical prediction of macaque expression using Calu-3 model. The Calu-3 expression data was clustered into different numbers of clusters (X axis) and used to infer models that were used to cross-predict expression in macaque. Individual genes are shown as rows and their performance in cross-prediction is indicated by color, from blue, -1.0, to yellow, 1.0 correlation between predicted and observed expression in macaques.

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Additional file 7:

Table S5; Top biological functions (as determined by IPA). Most statistically significant functions for set were determined and then sorted by # of genes within function. Redundant biological functions (with redundant gene content) were removed and table was limited to 10 biological functions.

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Additional file 8:

Known relationships between highly predicted genes. This network depicts all of the molecules within the gene set that were directly or indirectly related using information in the IPA knowledge base. Molecules shaded in grey are represented within the gene set that could be highly predicted in macaques by the Calu-3-based model. This illustrates the interactions between upstream regulators response (ATF3, FOS, JUN), several cytokines and chemokines, interferon-regulated molecules.

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Additional file 9:

Predicted versus observed expression profiles for IL-6 in mouse.

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Additional file 10:

Distribution of prediction scores. A. Histogram of cluster prediction correlations. The correlation of predicted to observed expression profiles was calculated for each cluster considered and is plotted as a histogram, where the frequency indicates the number of genes with that correlation. B. Histogram of gene correlation with predicted expression. The correlation of individual gene expression profiles with the predicted expression profile for the cluster that the gene is a member was calculated and is plotted as a histogram. C. Histogram of the cross-prediction scores. Cross-prediction scores (cluster prediction × gene correlation) were calculated for all genes in all clusters and are plotted as a histogram. The top × axis indicates the Z scores.

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