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Open Access Highly Accessed Methodology article

Cluster-based assessment of protein-protein interaction confidence

Atanas Kamburov1*, Arndt Grossmann2, Ralf Herwig1 and Ulrich Stelzl2*

Author Affiliations

1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Ihnestr. 63-73, Germany

2 Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Ihnestr. 63-73, Germany

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BMC Bioinformatics 2012, 13:262  doi:10.1186/1471-2105-13-262

Published: 10 October 2012

Additional files

Additional file 1:

Table S1. Interaction data sets merged to construct the Y2H-human network.The table lists the studies that contribute yeast-two-hybrid interactions for the merged Y2H-human network. The file is in XLS format and is viewable e.g. with LibreOffice or Microsoft Excel.

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Additional file 2:

Table S2. Properties of the Y2H-human and Mazloom networks. The table shows the properties of the human networks used in the analysis (analogous to Table 1 in the main text). The file is in XLS format and is viewable e.g. with LibreOffice or Microsoft Excel.

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Additional file 3:

Supplementary Text. This file contains additional text and figures demonstrating the validity of the partial random rewiring approach for clustering parameter optimization, as well as text and figures showing that CAPPIC scores can be used for interaction cluster de-noising. The file is in PDF format and is viewable e.g. with Adobe Reader.

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Additional file 4:

Figure S1. ROC plots with complex-based positive reference sets. Receiver operating characteristic analysis results for the yeast reference networks where complex-based positive reference sets have been used. Complexes were obtained from ref. [57] (A) and from ref. [58] (B). The figure is otherwise analogous to Figure 2.

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Additional file 5:

Figure S2. Cluster number and sizes for the yeast reference networks clustered with the optimal granularity. Yeast reference networks were clustered at the optimal inflation value into 10-50 interaction clusters. Here, the cluster sizes in terms of number of interactions (blue line, left-hand-side Y-axis) and number of genes/proteins (green line, right-hand-side Y-axis) per cluster are plotted.

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Additional file 6:

Figure S3. Distribution of CAPPIC scores for the hubs PHO85 and UBC7 in comparison to the whole data set.

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