Development of the first oligonucleotide microarray for global gene expression profiling in guinea pigs: defining the transcription signature of infectious diseases

Additional file 1:

Supporting Materials and Methods and Tables.

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Additional file 2:

Pulmonary gene expression signature of guinea pigs at 10 weeks post M. tuberculosis infection. The figure depicts the clustered heat maps for all the genes on the 44 K GPOM in case of infected guinea pigs compared to uninfected control. By using unsupervised hierarchical clustering algorithm, the most similar expression profiles are joined together to form a group. These are further joined in a tree structure, until all data forms a single group. Clustering is based on averaged distance between two clusters, which is the average of the pair-wise distance between entities in the two clusters. For measurement of similarity between conditions, Pearson coefficient correlation clustering algorithm is used. The color scheme for the hierarchical clustering is - yellow: no change in expression, magenta: higher expression in infected lungs relative to normal lungs and green: lower expression in infected samples relative to normal uninfected lungs. 1: Uninfected control; 2: Infected Lung 1; 3: Infected Lung 2; 4: Infected Lung 3.

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Additional file 3:

List of genes exhibiting significant transcriptional regulation in the lungs of M. tuberculosis infected guinea pigs compared to uninfected guinea pigs. The excel data sheets depict list of up and down regulated unique genes, for which, all the probes exhibited consist expression pattern. The expression values from multiple probes were averaged for a gene.

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Additional file 4:

Pathway analysis for the up and down regulated genes. The excel file describes the pathway analysis for the up and down regulated genes. The pathway analysis was performed by using Human Biointerpreter tool (http://genotypic.co.in/biointerpreter.html) based on KEGG database.

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Additional file 5:

Comparison of pulmonary transcriptional response of guinea pig, human, non-human primate and mouse to M. tuberculosis infection. The excel file depicts the comparison of up and down regulated genes from this guinea pig microarray study with those obtained from human, non-human primate and mouse microarray data available in the public database. The Venn diagrams depict the number of genes overlapping among different species.

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