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Open Access Highly Accessed Research article

A survey of protein interaction data and multigenic inherited disorders

Antonio Mora12, Katerina Michalickova3 and Ian M Donaldson12*

Author Affiliations

1 Department for Molecular Biosciences, University of Oslo, P.O. Box 1041 Blindern, 0316, Oslo, Norway

2 The Biotechnology Centre of Oslo, University of Oslo, P.O. Box 1125 Blindern, 0317, Oslo, Norway

3 Scientific Computing Group, University of Oslo, P.O. Box 1059 Blindern, Oslo, Norway

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BMC Bioinformatics 2013, 14:47  doi:10.1186/1471-2105-14-47

Published: 11 February 2013

Additional files

Additional file 1:

This is a plain text file that contains R code to reproduce all R analyses in the paper. See http://www.r-project.org/. webcite

Format: TXT Size: 23KB Download file

Open Data

Additional file 2:

Distribution of number of genes per disease group (DiG).

Format: PDF Size: 11KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Mapping of OMIM titles to disease groups and Entrez Gene identifiers.

Format: XLSX Size: 190KB Download file

Open Data

Additional file 4:

Summary of disease groups in terms of both genes and proteins.

Format: XLSX Size: 52KB Download file

Open Data

Additional file 5:

The file can be opened in Cytoscape (http://cytoscape.org webcite) to reproduce Figure 1 and explore disease groups and their overlaps.

Format: CYS Size: 324KB Download file

Open Data

Additional file 6:

Overlaps between disease groups and n-ary records showing best overlaps (icrigid) and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Additional information on n-ary records with the best overlap with a disease group can be found at http://wodaklab.org/iRefWeb/interaction/show/xxx webcite where xxx is the icrigid ( for example, http://wodaklab.org/iRefWeb/interaction/show/705064 webcite).

Format: XLSX Size: 49KB Download file

Open Data

Additional file 7:

The file can be opened in Cytoscape (http://cytoscape.org webcite) to reproduce Figure 3 and explore disease groups and their overlaps with n-ary data in iRefIndex.

Format: CYS Size: 3.6MB Download file

Open Data

Additional file 8:

Overlaps between disease groups and regenerated complex data showing best overlaps and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Example regenerated complexes have regular names that can be used to retrieve the binary interactions that make up the regenerated complex. For example: in the name “MI:0463(grid).pubmed:10722728.MI:0004 (affinity chromatography technology).10724593”, the BioGrid database has curated interactions from the paper with PubMed Identifier 10722728 where an affinity chromatography method was used to identify interactors of a common bait (icrogid: 10724593).

Format: XLSX Size: 49KB Download file

Open Data

Additional file 9:

Significance of overlaps between disease groups and binary data was calculated as described in the text. Number of interaction edges for each disease group is listed. Only those disease group overlaps with raw p-values less than 0.0004 are considered statistically significant.

Format: XLSX Size: 43KB Download file

Open Data

Additional file 10:

Each disease group is listed along with its number of genes, Entrez Gene IDs, and best overlaps with n-ary data and regenerated data and most significant raw p-value for binary data enrichment. Additional information on best overlapping n-ary record or regenerated complex can be found using the provided identifier as described in AF6 and AF8. Binary data corresponding to a disease group can be found using the iRefScape plugin for Cytoscape using the provided DiG ID or list of Gene IDs.

Format: XLSX Size: 58KB Download file

Open Data

Additional file 11:

Each disease group is listed along with the number of significant overlaps with KEGG pathway records before and after correction for multiple hypothesis testing. The KEGG entry identifier for the best overlapping pathway record is provided in column 3. For example 5200 is record hsa05200.

Format: XLSX Size: 42KB Download file

Open Data