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Large scale comparison of global gene expression patterns in human and mouse

Xiangqun Zheng-Bradley*, Johan Rung, Helen Parkinson and Alvis Brazma*

Author Affiliations

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK

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Genome Biology 2010, 11:R124  doi:10.1186/gb-2010-11-12-r124

Published: 23 December 2010

Additional files

Additional file 1:

PCA plot of the integrated mouse gene expression data matrix. The two axes are components 2 and 3; each dot represents a sample, colored by experiment accession number. While experiments with more than 15 samples are labeled as individual experiments, experiments with smaller numbers of samples are grouped into one category, 'small exp' (light brown). Tissue clusters observed in Figure 1 are circled. No apparent clustering of samples based on experiments is observed.

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Additional file 2:

Experiments and samples used for the mouse PCA.

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Additional file 3:

Distribution of gene expression variances for the top 50 principal components. The histograms were plotted for PCA results of the combined human mouse data matrix normalized by (a) probeset or (b) sample.

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Additional file 4:

PCA plot of a combined human and mouse gene expression data matrix (principal components 1 and 2). The samples are labeled by (a) species and (b) tissue type. Four major sample clusters are indicated: muscle/heart samples (red), nervous system samples (blue), liver samples (purple) and cell line samples (green). For these clusters, human and mouse samples exhibit subclustering in proximity to each other.

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Additional file 5:

PCA plots of a combined human and mouse gene expression data matrix with all samples. The samples are labeled by (a) species and (b) tissue type. Unlike previous PCA plots, samples such as mammary gland and hematopoietic system whose presentation is mostly one-sided in one species were removed from the analysis; this PCA included all high quality data from both human and mouse. The clustering of samples from nervous system (green), muscle/heart (lilac), cell lines (brown), and liver (pink) is still evident among the overwhelmingly dominant hematopoietic samples (blue) and mammary gland samples (turquoise). The corresponding human and mouse sample clusters resemble each other. Samples of unknown tissue type annotation are colored white and labeled as '0'.

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Additional file 6:

PCA plots of a combined human and mouse gene expression data matrix normalized by sample. The samples are labeled by (a) species and (b) tissue type. Mouse samples (black) and human samples (red) are well separated on the axis of component 1. Tissue clusters in the two species are projected to the second principal component in a similar order: nervous system (blue), muscle/heart (red), liver (purple) and cell lines (green).

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Additional file 7:

Hierarchical clustering heatmap of Pearson correlation coefficients between different types of tissues in human and mouse. Tissues in which human and mouse data clustered together are outlined by boxes.

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Additional file 8:

Distribution of corCor between human and mouse ortholog genes in specific tissues. The X-axis is the corCor value between human and mouse gene expression levels in (a) nervous system and (b) cell line samples. The Y-axis is the number of orthologs. In these analyses, corCor distribution is not very different from a randomized negative control (Figure 4a).

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Additional file 9:

Percentage of common genes in the top 10% most variable genes between different tissues of the same species, as well as between different tissues of human and mouse. The numbers in bold are those represented in the top 10% group in Figure 5.

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Additional file 10:

Functional analysis of orthologous genes shared between mouse and human in the top 10% most variable genes and the top 10% least variable genes. (a-c) The top 10% most variable genes and (d) the top 10% least variable genes: (a,d) nervous system; (b) muscle/heart; (c) liver. In (a-c), GO over-representation was sorted by corrected P-value and then by level of GO term enrichment; only the top ten categories are displayed. Genes with tissue-specific functions are colored in orange. The over-represented GO terms in (d) were sorted by count of genes in each category; the top categories are mostly housekeeping molecular functions.

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