Open Access Highly Accessed Methodology article

A novel method for cross-species gene expression analysis

Erik Kristiansson1*, Tobias Österlund2, Lina Gunnarsson3, Gabriella Arne4, D G Joakim Larsson5 and Olle Nerman1

Author Affiliations

1 Department of Mathematical Statistics, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden

2 Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden

3 Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden

4 Sahlgrenska Cancer Center, Department of Pathology, Sahlgrenska Academy at The University of Gothenburg, Gothenburg, Sweden

5 Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden

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BMC Bioinformatics 2013, 14:70  doi:10.1186/1471-2105-14-70

Published: 27 February 2013

Additional files

Additional file 1:

Additional figures demonstrating the power of the method using simulations. Power characteristics for the proposed and previously suggested methods. The file contains results from the following simulations: (1) multiple in-paralogs with similar expression profile (2) multiple in-paralogs with divergent expression profile, (3) noise with thick tails (t-distribution with five degrees of freedom), (4) errors in homology structure, error rate=0.1 and (5) errors in the homology structure, error rate=0.5.

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Additional file 2:

List of analyzed homology groups from the meta-analysis of heat stress experiments. Results for each homology group based on heat stress experiments performed in eight different species. The list contains combined p-value and false discovery rate as well as individual p-values from each experiment.

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Additional file 3:

Results of the functional enrichment of Gene Ontology terms. Results from the Gene Ontology (GO) term enrichment analysis of the significant homology groups from the heat stress analysis. The file contains results from the biological process (BP), cellular component (CC) and molecular function (MF) ontologies.

Format: XLSX Size: 929KB Download file

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Additional file 4:

List of analyzed homology groups from the meta-analysis of aquatic vertebrates exposed to estrogens. Results for each homology group based on estrogen exposure experiments performed in four aquatic vertebrates. The list contains combined p-value and false discovery rate as well as individual p-values from each experiment.

Format: XLSX Size: 1.1MB Download file

Open Data