Methodology article
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
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* Corresponding author: Shoshana J Wodak shoshana@sickkids.ca
1 Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto Ontario, M5G 1X8, Canada
2 Department of Biochemistry University of Toronto, 1 King's College Circle, Toronto Ontario, M5S 1A8, Canada
3 Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto Ontario, M5S 1A8, Canada
BMC Bioinformatics 2009, 10:99 doi:10.1186/1471-2105-10-99
Published: 30 March 2009Additional files
Additional File 1:
Curated Complexes. Curated complexes[28] used to generate the unweighted networks, and taken as the reference set for computing the Geometric Accuracy (Acc) and Separation (Sep) values (see main text for detail).
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Additional File 2:
Clustering Results, Unweighted Network. AP and MCL results for all parameters tested, at all noise levels for the unweighted network. Columns descriptions are listed in the 'col_descriptions' worksheet tab of this spreadsheet. See also reference [15] and main text for descriptions of PPV, Sensitivity, Acc, SepCl, SepCo, and Sep.
Format: XLS Size: 330KB Download file
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Additional File 3:
MCL Human PPI Size Distribution. Size distributions of clusters in partitions computed by MCL on a human PPI network (15 982 interactions and 5850 proteins) extracted from version 2.0.50 of the Biogrid database[33]. AP did not converge for this network, precluding any comparison.
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Additional File 4:
Supplementary Figures. Supplementary figures referred to in the main text.
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Additional File 5:
Clustering Results, Weighted Network. AP and MCL results for all parameters tested, at all noise levels for the weighted network. Column descriptions are given in the 'col_descriptions' worksheet tab of this spreadsheet. See also reference [15] and main text for descriptions of PPV, Sensitivity, Acc, SepCl, SepCo, and Sep.
Format: XLS Size: 121KB Download file
This file can be viewed with: Microsoft Excel Viewer