Open Access Highly Accessed Research article

Genetic architecture of gene expression in ovine skeletal muscle

Lisette JA Kogelman12, Keren Byrne3, Tony Vuocolo3, Nathan S Watson-Haigh17, Haja N Kadarmideen14, James W Kijas3, Hutton V Oddy5, Graham E Gardner6, Cedric Gondro5 and Ross L Tellam3*

Author Affiliations

1 CSIRO Livestock Industries, ATSIP, PMB CSIRO Aitkenvale, Townsville QLD 4814, Australia

2 Wageningen University and Research Centre (WUR), Animal Breeding and Genetics, Wageningen, The Netherlands

3 CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Brisbane, QLD 4067, Australia

4 Division of Genetics and Bioinformatics, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark

5 School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia

6 School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, WA 6150, Australia

7 The Australian Wine Research Institute, P.O. Box 197, Glen Osmond, SA 5064, Australia

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BMC Genomics 2011, 12:607  doi:10.1186/1471-2164-12-607

Published: 15 December 2011

Additional files

Additional file 1:

Genes in the identified WGCNA modules and the differential gene co-expression network modules. This file lists the genes present in the identified WGCNA modules and the differential gene co-expression network modules. Each module was identified by a colour name. The Affymetrix probe set, gene symbol and gene name are listed. Some probe sets could not be uniquely annotated.

Format: XLSX Size: 40KB Download file

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Additional file 2:

Functional annotation clustering of genes present in the identified WGCNA modules. Summary table listing enriched functional annotation clusters and functional terms associated with genes in the identified WGCNA modules. The analysis was performed using DAVID analysis tools, which provide a higher order perspective of functional term enrichments as enriched clusters of terms [18]. Conservative parameters were used in the analysis. P-values were corrected for multiple testing using the Benjamini correction. The enrichment score for a Functional Annotation Cluster is the -log (geometric mean of the term P-values within the cluster). Enrichment scores ≥1.0 were considered significant. No enriched functional annotation clusters were identified for genes in the VioletWGCNA module using these parameters.

Format: XLSX Size: 25KB Download file

Open Data

Additional file 3:

Enriched motifs present in the promoters of genes in the identified WGCNA and differentially connected modules. Genes present in each of the identified WGCNA and differentially connected modules were examined by using GSEA for enrichment of conserved cis-acting regulatory motifs [19]. The database within GSEA included gene-associated anonymous motifs conserved in the human, mouse, rat and dog genomes and conserved gene-associated transcription factor binding sites. The motifs were restricted to a 'promoter' sequence window corresponding to ± 2 kb of the transcription start site. P-values ≤ 0.05 were considered significant.

Format: XLSX Size: 21KB Download file

Open Data

Additional file 4:

Hierarchical tree graphs of over-represented GO terms for genes in the LightgreenWGCNA module. Hierarchical tree graphs of over-represented gene ontology (GO) terms for genes in the LightgreenWGCNA module were constructed using AgriGO [16]. Boxes in the graphs represent GO terms labelled by GO number, term definition and statistical information. Significant terms (adjusted P ≤ 0.05) are coloured. The degree of colour saturation of a box is positively correlated to the enrichment level of the term. Solid, dashed, and dotted lines represent two, one and zero enriched terms at both ends connected by the line, respectively. GO categories: (a) Molecular Function; (b) Biological Process; (c) Cellular Component.

Format: TIFF Size: 1.4MB Download file

Open Data

Additional file 5:

Hierarchical tree graphs of over-represented GO terms for genes in the VioletWGCNA module. Hierarchical tree graphs of over-represented gene ontology (GO) terms for genes in the VioletWGCNA module were constructed using AgriGO [16]. Boxes in the graphs represent GO terms labelled by GO number, term definition and statistical information. The analysis was performed using less stringent parameters (adjusted P < 0.1 and ≥ 2 genes/term) than the default parameters. Significant terms are coloured. The degree of colour saturation of a box is positively correlated to the enrichment level of the term. Solid, dashed, and dotted lines represent two, one and zero enriched terms at both ends connected by the line, respectively. GO categories: (a) Biological Process; (b) Cellular Component.

Format: TIFF Size: 1.2MB Download file

Open Data

Additional file 6:

Hierarchical tree graphs of over-represented GO terms for genes in the VioletDiff module. Hierarchical tree graphs of over-represented gene ontology (GO) terms for genes in the VioletDiff module were constructed using AgriGO [16]. Boxes in the graph represent GO terms labelled by GO number, term definition and statistical information. The analysis was performed using default parameters. Significant terms are coloured (adjusted P ≤ 0.05). The degree of colour saturation of a box is positively correlated to the enrichment level of the term. Solid, dashed, and dotted lines represent two, one and zero enriched terms at both ends connected by the line, respectively. Only the Cellular Component GO category was significant.

Format: TIFF Size: 783KB Download file

Open Data

Additional file 7:

Functional annotation clustering of genes present in the differential gene co-expression modules. Summary table listing enriched functional annotation clusters and functional terms significantly associated with the genes in the identified differential gene co-expression modules. The analysis was performed using DAVID analysis tools which provide a higher order perspective of functional term enrichments [18]. Conservative analysis parameters were used in the analysis. P-values were corrected for multiple testing using the Benjamini correction. The enrichment score for a Functional Annotation Cluster is the -log (geometric mean of the term P-values within the cluster). Enrichment scores ≥ 1.0 were considered significant.

Format: XLSX Size: 43KB Download file

Open Data

Additional file 8:

Hierarchical tree graphs of over-represented GO terms for genes in the Light-greenDiff module. Hierarchical tree graphs of over-represented gene ontology (GO) terms for genes in the Light-greenDiff module were constructed using AgriGO [16]. Boxes in the graphs represent GO terms labelled by GO number, term definition and statistical information. The analysis was performed using default parameters. Significant terms are coloured (adjusted P ≤ 0.05). The degree of colour saturation of a box is positively correlated to the enrichment level of the term. Solid, dashed, and dotted lines represent two, one and zero enriched terms at both ends connected by the line, respectively.

Format: TIFF Size: 1.7MB Download file

Open Data

Additional file 9:

Hierarchical tree graphs of over-represented GO terms for genes in the Green-yellowDiff module. Hierarchical tree graphs of over-represented gene ontology (GO) terms for genes in the Green-yellowDiff module were constructed using AgriGO [16]. Boxes in the graphs represent GO terms labelled by GO number, term definition and statistical information. The analysis was performed using default parameters. Significant terms are coloured (adjusted P ≤ 0.05). The degree of colour saturation of a box is positively correlated to the enrichment level of the term. Solid, dashed, and dotted lines represent two, one and zero enriched terms at both ends connected by the line, respectively. Only terms in the Biological Process GO category were significant.

Format: TIFF Size: 876KB Download file

Open Data