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Zanivan S
Cascone I
Peyron C
Molineris I
Marchio S
Caselle M
Bussolino F

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Zanivan S
Cascone I
Peyron C
Molineris I
Marchio S
Caselle M
Bussolino F
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A new computational approach to analyze human protein complexes and predict novel protein interactions

Sara Zanivan¹^,2 , Ilaria Cascone¹^,3 , Chiara Peyron⁴ , Ivan Molineris⁴ , Serena Marchio¹ , Michele Caselle^*⁴ and Federico Bussolino^*¹

¹Department of Oncological Sciences and Division of Molecular Angiogenesis, Institute for Cancer Research and Treatment (IRCC), University of Torino Medical School, Strada Provinciale, I-10060 Candiolo (Turin), Italy

²Max-Planck Institute for Biochemistry, Department of Proteomics and Signal Transduction, Am. Klopferspitz, D-82152 Martinsried, Germany

³Inserm U528, Institut Curie, 75248 Paris, France

⁴Department of Theoretical Physics, University of Torino and INFN, Via P Giuria 1, I-10125 Turin, Italy

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R256doi:10.1186/gb-2007-8-12-r256


Published:	4 December 2007

Subject areas: Bioinformatics, Genome studies

Additional files

Additional data file 1:

P values obtained with the expression peaks method in each time interval of the cell-cycle or with Pearson correlation coefficient throughout the cell-cycle (Cell-cycle column). (a) Thy-Thy2; (b) Thy-Thy3.

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Additional data file 2:

(a, d) Thy-Thy2 dataset; (b, e) Thy-Thy3 dataset; (c, f) Thy-Noc dataset. ND, not defined.

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Additional data file 3:

For each protein complex, the percentage of its synchronously peaking genes in each time interval is reported. (a) Thy-Thy2; (b) Thy-Thy3.

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Additional data file 4:

The number of complexes with a best p value equal to or lower than the corresponding one on the x-axis for three non-synchronized and stressed HeLa datasets at a fixed FDR. (a) Crowding; (b) H₂O₂; (c) menadione.

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Additional data file 5:

A subset of the human protein complexes was analyzed with PEGO. For each protein complex, the GO Biological process term(s), G, and the time interval, T, if present, are indicated, displaying best p value lower than 0.05 after statistical analysis by means of hypergeometric distribution (Table 2, and Additional data files 1 and 7). These are the input parameters used to obtain Additional data file 6. (a) Thy-Thy2; (b) Thy-Thy3; (c) Thy-Noc. An asterisk indicates that the p value for the expression peak was between 0.1 and 0.05.

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Additional data file 6:

Time interval (T) with best p value and GO Biological process term (G) with best p value were used to query PEGO (Additional data file 5). T genes, number of genes in the dataset with expression peak in T; G genes, number of genes in the dataset annotated at G; I genes, number of genes in the dataset with expression peak in T and GO G; T complex genes, number of genes of the protein complex with expression peak in T; G complex genes, number of genes of the protein complex with GO G; I complex genes, number of genes of the protein complex with expression peak in T and GO G; T % complex genes, (T complex genes/T genes) × 100; G % complex genes, (G complex genes/G genes) × 100; I % complex genes, I complex genes/I genes) × 100; % complex genes, percentage of genes of the protein complex with expression peak in T and GO G. An asterisk indicates that the p value for the expression peak is between 0.1 and 0.05. (a) Thy-Thy2; (b) Thy-Thy3; (c) Thy-Noc.

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Additional data file 7:

The first column lists the complexes (the same as analyzed in Additional data file 5), and the second, third and fourth columns provide information on the ontology and GO category. In the following four columns we report the input information for p value evaluation using the hypergeometric distribution (Additional data file 12) and in the last column the corresponding p values. Only GO terms with a p value with exponent lower or equal to E-05 are reported. (a) Thy-Thy2; (b) Thy-Thy3; (c) Thy-Noc.

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Additional data file 8:

Text: List of genes with an expression peak at the 14 h-12 h interval in the Thy-Noc dataset and annotated as Organelle organization and biogenesis [GO:0006996] for the Biological process term and as Cytoskeleton [GO:0005856] or Cytoplasm [GO:0005737] for the Cellular component term.

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Additional data file 9:

Images show a broader molecular weight range of the blots in Figure 4. (a) HeLa cell lysate was immunoprecipitated with anti-PAK1 antibody or rabbit serum and blotted with anti α-tubulin antibody. (b) HeLa cell lysate blotted with anti-PAK1 antibody. The time exposure of (b) is higher than in Figure 4 to better evaluate the specificity of the antibody.

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Additional data file 10:

Entrez Gene IDs of all components of each protein complex analyzed.

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Additional data file 11:

For each gene, indicated by its Entrez Gene ID, the corresponding IMAGE IDs present in each dataset is reported. (a) Thy-Thy2; (b) Thy-Thy3; (c) Thy-Noc.

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Additional data file 12:

Supplemental Materials and methods.

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