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Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

Bolan Linghu1, Evan S Snitkin1, Zhenjun Hu1, Yu Xia12 and Charles DeLisi1*

Author Affiliations

1 Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA

2 Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA

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Genome Biology 2009, 10:R91  doi:10.1186/gb-2009-10-9-r91

Published: 3 September 2009

Additional files

Additional data file 1:

Column 1, Entrez Gene ID for gene A; column 2, Entrez Gene ID for gene B; column 3, functional linkage weight (log likelihood ratio of the naïve Bayes integration).

Format: TXT Size: 1KB Download file

Open Data

Additional data file 2:

Known (seed) disease genes associated with each of the 110 diseases.

Format: XLS Size: 264KB Download file

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Additional data file 3:

A WinRAR archive composed of a readme.txt file and 110 prediction files for the 110 diseases. For each disease, we list the top 100 ranked new candidate disease genes not included in the disease seed gene set. The description of the prediction files is provided in the readme.txt file.

Format: RAR Size: 213KB Download file

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Additional data file 4:

Plot of precision versus rank cutoff for the top 100 predicted candidate disease genes for each of the 110 diseases.

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Additional data file 5:

Supplemental methods, supplementary results, supplementary Figures S1 to S9, and supplementary Table S1 to S4.

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Additional data file 6:

Recently identified disease genes and landmark references dated after January 2007.

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Additional data file 7:

The 22 predicted obesity genes among the top 100 predicted gene list that overlap with the obesity genes collected from literature by Hanock et al. [58].

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Additional data file 8:

Mutual predictability scores for all the possible disease pairs between the 110 diseases.

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Additional data file 9:

The top 100 disease pairs with the highest mutual predictability scores and the supporting evidence for the association.

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Additional data file 10:

Disease clusters, their disease members, and evidence supporting the associations in Figure S9 of Additional data file 5 and Figure 8a.

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Additional data file 11:

The 53 informative GO terms used to define the gold standard sets for the naïve Bayes integration.

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Additional data file 12:

Pearson correlation coefficients between the 16 features used for the naïve Bayes integration.

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