Clustering by common friends finds locally significant proteins mediating modules
Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, Michael Schroeder
Supplementary Information
Results for the Von Mering et al. PIN dataset (2002).
List of 'mediators', including
degrees and degree ranges, for the Gavin et al. PIN dataset (2006), interpreted via the matrix model:
The MULIC algorithm produced 274 clusters on the Gavin et al. PIN dataset.
The cluster sizes ranged from 2-50 proteins. We identified 985 mediator proteins.
Mediators are widely dispersed across all degree ranges.
The number of proteins that have degree 1 in this dataset (interpreted via the matrix model) is 171 out
of 2551 proteins in total (6.7%).
Protein Names of Clusters and Mediators: one mediators-cluster pair per line
Outliers: Protein Names
List of all Protein Names
GeneOntology(GO) Ancestry Relationships / Mappings of GO IDs to GO term names
All P-values of GO annotations in clusters' member proteins and mediators
Significant P-values (-log p-value >=2) of GO annotations in clusters' member proteins and mediators
Significant P-values (-log p-value >=3) of GO annotations in clusters' member proteins and mediators
All P-values of GO annotations in clusters' member proteins and mediators, mapped to GO level 7
All P-values of GO annotations in clusters' member proteins and mediators, mapped to GO level 9
All P-values of GO annotations in clusters' mediators
Significant P-values (-log p-value >=2) of GO annotations in clusters' mediators
All P-values of GO annotations in clusters' mediators, mapped to GO level 7
All P-values of GO annotations in clusters' mediators, mapped to GO level 9
All P-values of GO annotations in clusters' member proteins
Significant P-values (-log p-value >=2) of GO annotations in clusters' member proteins
All P-values of GO annotations in clusters' member proteins, mapped to GO level 7
All P-values of GO annotations in clusters' member proteins, mapped to GO level 9
Overlaps of clusters/mediators with complexes(cores/modules/attachments) in yeast dataset by Gavin et al. (2006)
GO annotation cross-talks between clusters and mediators (organized by location and levels of Gene Ontology)
Gavin et al. PIN dataset clustered (2006). Interpreted via the matrix model. Interactions of all confidences were included.
Clustering source code (C++)