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Open Access Highly Accessed Research article

From networks of protein interactions to networks of functional dependencies

Davide Luciani1 and Gianfranco Bazzoni2*

Author Affiliations

1 Unit of Clinical Knowledge Engineering, Mario Negri Institute of Pharmacological Research, Milan, I-20156, Italy

2 Laboratory of Systems Biology, Mario Negri Institute of Pharmacological Research, Milan, I-20156, Italy

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BMC Systems Biology 2012, 6:44  doi:10.1186/1752-0509-6-44

Published: 20 May 2012

Additional files

Additional file 1 :

The proteins of the peroxisomal PPI network (xls). The table reports all the core and neighbor proteins of the peroxisomal PPI network shown in Additional file 2, with the annotation(s) in the ‘cellular component’ ontology of GO (see last page of the table for explanation). The annotations are ‘Yeast GO Slim’ terms, except the ones in italics, which are child terms of the slim term GO:0005777 (‘Peroxisome’). k is the connectivity degree of each protein, i.e., its number of direct neighbors in the network.

Format: XLS Size: 98KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2 :

The peroxisomal PPI network (jpg). The PPI network comprises peroxisomal core proteins and their direct neighbors (green and yellow circles, respectively), as well as the PPI that have been detected by binary (red lines) or cluster (blue lines) assay (see also Table 1 of the main text). The size of each node is proportional to the k value of the corresponding protein.

Format: JPEG Size: 1016KB Download file

Open Data

Additional file 3 :

Node and edge distribution in the peroxisome PG at different NTS (jpg).The number of edges (top) and FN (bottom) in the peroxisome PG is shown as a function of the NTS.

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Additional file 4 :

FN and edges of the peroxisome PG (pdf). The file describes the FN and edges of the peroxisome PG (displayed in Figure 3 of the main text), the physical links underlying the edges (crossing PPI and/or shared proteins), as well as their biochemical basis and biological significance [38-75].

Format: DOC Size: 198KB Download file

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Additional file 5 :

FN and edges of the cellular bud and cell budding PG (pdf). The file describes the FN and the edges of the cellular bud and cell budding PG (displayed in Figure 5A and Figure 5B of the main text, respectively), the physical links underlying the edges (crossing PPI and/or shared proteins), as well as their biochemical basis and biological significance [76-94].

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Additional file 6 :

The FN of the peroxisome PG (jpg). The FN of the peroxisome PG (displayed in Figure 3 of the main text) are shown with their protein contents, definitive labels and NTS. As in the Additional file 2, green and yellow circles represent core and neighbor proteins, respectively. Also, red and blue lines represent PPI detected by binary or cluster assays, respectively.

Format: JPEG Size: 685KB Download file

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Additional file 7 :

Directed acyclic graphs in the peroxisome PG (xls). The table reports the node identity of the different types of DAG shown schematically in Figure 4A of the main text.

Format: XLS Size: 62KB Download file

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Additional file 8 :

Comparative analysis (pdf). The file describes the network analysis-based comparison of PG obtained with our method and with the method described in reference 5.

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