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A compendium of canine normal tissue gene expression.

Briggs J, Paoloni M, Chen QR, Wen X, Khan J, Khanna C - PLoS ONE (2011)

Bottom Line: Public access, using infrastructure identical to that currently in use for human normal tissues, has been established and allows for additional comparisons across species.These data advance our understanding of the canine genome through a comprehensive analysis of gene expression in a diverse set of tissues, contributing to improved functional annotation that has been lacking.Importantly, it will be used to inform future studies of disease in the dog as a model for human translational research and provides a novel resource to the community at large.

View Article: PubMed Central - PubMed

Affiliation: Tumor and Metastasis Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT

Background: Our understanding of disease is increasingly informed by changes in gene expression between normal and abnormal tissues. The release of the canine genome sequence in 2005 provided an opportunity to better understand human health and disease using the dog as clinically relevant model. Accordingly, we now present the first genome-wide, canine normal tissue gene expression compendium with corresponding human cross-species analysis.

Methodology/principal findings: The Affymetrix platform was utilized to catalogue gene expression signatures of 10 normal canine tissues including: liver, kidney, heart, lung, cerebrum, lymph node, spleen, jejunum, pancreas and skeletal muscle. The quality of the database was assessed in several ways. Organ defining gene sets were identified for each tissue and functional enrichment analysis revealed themes consistent with known physio-anatomic functions for each organ. In addition, a comparison of orthologous gene expression between matched canine and human normal tissues uncovered remarkable similarity. To demonstrate the utility of this dataset, novel canine gene annotations were established based on comparative analysis of dog and human tissue selective gene expression and manual curation of canine probeset mapping. Public access, using infrastructure identical to that currently in use for human normal tissues, has been established and allows for additional comparisons across species.

Conclusions/significance: These data advance our understanding of the canine genome through a comprehensive analysis of gene expression in a diverse set of tissues, contributing to improved functional annotation that has been lacking. Importantly, it will be used to inform future studies of disease in the dog as a model for human translational research and provides a novel resource to the community at large.

Show MeSH
Principle component analysis and hierarchical clustering define                            relationships between canine normal tissues.mRNA expression for 39 samples from ten pathologically normal canine                            tissues were analyzed using the Affymetrix Canine Version 2.0                            GeneChip®. Probesets differentially expressed in at least one tissue                            (as described in the Methods) were included in the analysis (23,070                            probesets corresponding to 10,878 unique gene symbols). A.                            Samples were analyzed by principle component analysis (PCA) to                            characterize relationships between biological replicates for each                            tissue. Each sphere represents an individual sample, colored by tissue                            and ellipses correspond to two standard deviations of the tissue group                            mean. B. Hierarchical clustering of samples was conducted                            with distances calculated using Pearson correlation metrics and clusters                            joined using Ward linkage. Bootstrap re-sampling was conducted (1,000                            iterations) in order to determine cluster stability. C.                            Heatmap demonstrating tissue selective gene expression. Following ANOVA                            to determine differential expression based on tissue type, results were                            filtered based on FDR = 0.001 as well as expression                            thresholds of greater than 10-fold expression over the mean of all other                            tissues and no greater than 3-fold over the mean in any other tissue.                            This final list of tissue selective probesets was rank ordered according                            to fold-expression with sample order determined by the previous                            bootstrapped hierarchical clustering. Red indicates upregulated and                            green represents downregulated relative to the mean expression in all                            tissues. Numbers next to the heatmap indicate the number of tissue                            selective probesets in a cluster.
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pone-0017107-g001: Principle component analysis and hierarchical clustering define relationships between canine normal tissues.mRNA expression for 39 samples from ten pathologically normal canine tissues were analyzed using the Affymetrix Canine Version 2.0 GeneChip®. Probesets differentially expressed in at least one tissue (as described in the Methods) were included in the analysis (23,070 probesets corresponding to 10,878 unique gene symbols). A. Samples were analyzed by principle component analysis (PCA) to characterize relationships between biological replicates for each tissue. Each sphere represents an individual sample, colored by tissue and ellipses correspond to two standard deviations of the tissue group mean. B. Hierarchical clustering of samples was conducted with distances calculated using Pearson correlation metrics and clusters joined using Ward linkage. Bootstrap re-sampling was conducted (1,000 iterations) in order to determine cluster stability. C. Heatmap demonstrating tissue selective gene expression. Following ANOVA to determine differential expression based on tissue type, results were filtered based on FDR = 0.001 as well as expression thresholds of greater than 10-fold expression over the mean of all other tissues and no greater than 3-fold over the mean in any other tissue. This final list of tissue selective probesets was rank ordered according to fold-expression with sample order determined by the previous bootstrapped hierarchical clustering. Red indicates upregulated and green represents downregulated relative to the mean expression in all tissues. Numbers next to the heatmap indicate the number of tissue selective probesets in a cluster.

Mentions: A comparison of gene expression profiles for ten normal canine organs was undertaken using an ANOVA model to assess the informative value of this data set. Consistent with previous studies in humans, >50% of all canine probesets (23,070) demonstrated differential expression based on tissue type and this corresponds to 10,878 unique gene symbols. [15], [19], [20] To further validate the utility of these data and to characterize relationships between biological replicates, samples were analyzed by principle component analysis (PCA) (Fig. 1A and Fig. S1) and hierarchical clustering (HC) (Fig. 1B) using those probesets differentially expressed in at least one tissue. As shown in Fig. 1A samples grouped according to organ type with greater than 47% of the variability explained by the first three principle components. Multi-level bootstrap re-sampling was then conducted on hierarchical clustering results in order to determine the reproducibility of cluster assignment. As shown in Fig. 1B, replicate samples again grouped together according to organ type (>95% confidence at each branch point). Identical results were observed when using all probesets (data not shown). In addition, tissues with a common developmental origin and/or anatomical function grouped together. For example, mesoderm derived heart and skeletal muscle group together as do the functionally related immune organs lymph node and spleen.


A compendium of canine normal tissue gene expression.

Briggs J, Paoloni M, Chen QR, Wen X, Khan J, Khanna C - PLoS ONE (2011)

Principle component analysis and hierarchical clustering define                            relationships between canine normal tissues.mRNA expression for 39 samples from ten pathologically normal canine                            tissues were analyzed using the Affymetrix Canine Version 2.0                            GeneChip®. Probesets differentially expressed in at least one tissue                            (as described in the Methods) were included in the analysis (23,070                            probesets corresponding to 10,878 unique gene symbols). A.                            Samples were analyzed by principle component analysis (PCA) to                            characterize relationships between biological replicates for each                            tissue. Each sphere represents an individual sample, colored by tissue                            and ellipses correspond to two standard deviations of the tissue group                            mean. B. Hierarchical clustering of samples was conducted                            with distances calculated using Pearson correlation metrics and clusters                            joined using Ward linkage. Bootstrap re-sampling was conducted (1,000                            iterations) in order to determine cluster stability. C.                            Heatmap demonstrating tissue selective gene expression. Following ANOVA                            to determine differential expression based on tissue type, results were                            filtered based on FDR = 0.001 as well as expression                            thresholds of greater than 10-fold expression over the mean of all other                            tissues and no greater than 3-fold over the mean in any other tissue.                            This final list of tissue selective probesets was rank ordered according                            to fold-expression with sample order determined by the previous                            bootstrapped hierarchical clustering. Red indicates upregulated and                            green represents downregulated relative to the mean expression in all                            tissues. Numbers next to the heatmap indicate the number of tissue                            selective probesets in a cluster.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3104984&req=5

pone-0017107-g001: Principle component analysis and hierarchical clustering define relationships between canine normal tissues.mRNA expression for 39 samples from ten pathologically normal canine tissues were analyzed using the Affymetrix Canine Version 2.0 GeneChip®. Probesets differentially expressed in at least one tissue (as described in the Methods) were included in the analysis (23,070 probesets corresponding to 10,878 unique gene symbols). A. Samples were analyzed by principle component analysis (PCA) to characterize relationships between biological replicates for each tissue. Each sphere represents an individual sample, colored by tissue and ellipses correspond to two standard deviations of the tissue group mean. B. Hierarchical clustering of samples was conducted with distances calculated using Pearson correlation metrics and clusters joined using Ward linkage. Bootstrap re-sampling was conducted (1,000 iterations) in order to determine cluster stability. C. Heatmap demonstrating tissue selective gene expression. Following ANOVA to determine differential expression based on tissue type, results were filtered based on FDR = 0.001 as well as expression thresholds of greater than 10-fold expression over the mean of all other tissues and no greater than 3-fold over the mean in any other tissue. This final list of tissue selective probesets was rank ordered according to fold-expression with sample order determined by the previous bootstrapped hierarchical clustering. Red indicates upregulated and green represents downregulated relative to the mean expression in all tissues. Numbers next to the heatmap indicate the number of tissue selective probesets in a cluster.
Mentions: A comparison of gene expression profiles for ten normal canine organs was undertaken using an ANOVA model to assess the informative value of this data set. Consistent with previous studies in humans, >50% of all canine probesets (23,070) demonstrated differential expression based on tissue type and this corresponds to 10,878 unique gene symbols. [15], [19], [20] To further validate the utility of these data and to characterize relationships between biological replicates, samples were analyzed by principle component analysis (PCA) (Fig. 1A and Fig. S1) and hierarchical clustering (HC) (Fig. 1B) using those probesets differentially expressed in at least one tissue. As shown in Fig. 1A samples grouped according to organ type with greater than 47% of the variability explained by the first three principle components. Multi-level bootstrap re-sampling was then conducted on hierarchical clustering results in order to determine the reproducibility of cluster assignment. As shown in Fig. 1B, replicate samples again grouped together according to organ type (>95% confidence at each branch point). Identical results were observed when using all probesets (data not shown). In addition, tissues with a common developmental origin and/or anatomical function grouped together. For example, mesoderm derived heart and skeletal muscle group together as do the functionally related immune organs lymph node and spleen.

Bottom Line: Public access, using infrastructure identical to that currently in use for human normal tissues, has been established and allows for additional comparisons across species.These data advance our understanding of the canine genome through a comprehensive analysis of gene expression in a diverse set of tissues, contributing to improved functional annotation that has been lacking.Importantly, it will be used to inform future studies of disease in the dog as a model for human translational research and provides a novel resource to the community at large.

View Article: PubMed Central - PubMed

Affiliation: Tumor and Metastasis Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT

Background: Our understanding of disease is increasingly informed by changes in gene expression between normal and abnormal tissues. The release of the canine genome sequence in 2005 provided an opportunity to better understand human health and disease using the dog as clinically relevant model. Accordingly, we now present the first genome-wide, canine normal tissue gene expression compendium with corresponding human cross-species analysis.

Methodology/principal findings: The Affymetrix platform was utilized to catalogue gene expression signatures of 10 normal canine tissues including: liver, kidney, heart, lung, cerebrum, lymph node, spleen, jejunum, pancreas and skeletal muscle. The quality of the database was assessed in several ways. Organ defining gene sets were identified for each tissue and functional enrichment analysis revealed themes consistent with known physio-anatomic functions for each organ. In addition, a comparison of orthologous gene expression between matched canine and human normal tissues uncovered remarkable similarity. To demonstrate the utility of this dataset, novel canine gene annotations were established based on comparative analysis of dog and human tissue selective gene expression and manual curation of canine probeset mapping. Public access, using infrastructure identical to that currently in use for human normal tissues, has been established and allows for additional comparisons across species.

Conclusions/significance: These data advance our understanding of the canine genome through a comprehensive analysis of gene expression in a diverse set of tissues, contributing to improved functional annotation that has been lacking. Importantly, it will be used to inform future studies of disease in the dog as a model for human translational research and provides a novel resource to the community at large.

Show MeSH