Improved human disease candidate gene prioritization using mouse phenotype

doi:10.1186/1471-2105-8-392

BMC Bioinformatics

Volume 8

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Research article

Improved human disease candidate gene prioritization using mouse phenotype

Jing Chen¹^,2 , Huan Xu¹ , Bruce J Aronow¹^,2^,3 and Anil G Jegga¹^,3

¹Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA

²Department of Biomedical Engineering, University of Cincinnati, Cincinnati, USA

³Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:392doi:10.1186/1471-2105-8-392


Published:	16 October 2007

Additional files

Additional file 1:

Comparison of ToppGene with other prioritization approaches – Workflow. This figure shows the details of the comparisons we performed to evaluate our approach with respect to other similar gene prioritization approaches.

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Additional file 2:

List and ranking of genes in the 19 disease training sets used for validation. This file has the list of genes in the 19 disease training sets (randomly derived from Genetic Association Database, GAD and Online Mendelian Inheritance in Man, OMIM) used for validation along with the ranking of the "target" genes in random cross-validation.

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Additional file 3:

List and ranking of "target" genes in locus-region cross-validation using different feature sets. This file has the details of the ranking of the "target" genes in locus-region cross-validation using different gene feature sets. When MP or PubMed annotations were excluded in the prioritization, the prioritization performance dropped significantly.

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Additional file 4:

Comparison of relative rankings of "target" genes of congenital heart disease using SUSPECTS, ENDEAVOUR and ToppGene. The data provided represent the ranking results of "target" genes of congenital heart disease using SUSPECTS, ENDEAVOUR and ToppGene applications.

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Additional file 5:

Comparison of relative rankings of "target" genes of diabetic retinopathy using SUSPECTS, ENDEAVOUR and ToppGene. The data provided represent the ranking results of "target" genes of diabetic retinopathy using SUSPECTS, ENDEAVOUR and ToppGene applications.

Format: DOC Size: 62KB Download file

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Additional file 6:

Pairwise Pearson correlation test result of the p-values of all the 7 features used for candidate gene prioritization. This figure shows the pairwise Pearson correlation test result of the p-values of all the features used for candidate gene prioritization.

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