Research article
An evolutionary and structural characterization of mammalian protein complex organization
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* Corresponding author: Dmitrij Frishman d.frishman@wzw.tum.de
- † Equal contributors
1 Helmholtz Center Munich – German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1 D-85764 Neuherberg, Germany
2 Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, 85350 Freising, Germany
3 Max-Planck-Institute for Dynamics and Self-Organization, Bunsenstrasse 10, 37073 Göttingen, Germany
BMC Genomics 2008, 9:629 doi:10.1186/1471-2164-9-629
Published: 23 December 2008Additional files
Additional File 1:
Description of the protein complex data. A detailed description of annotated and random complex data used.
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Additional File 2:
Benchmark of PSIPRED. A benchmark of PSIPRED's ability to predict secondary structure content from protein sequences is provided.
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Additional File 3:
Yeast complex complexity and participation distributions. The distribution of yeast complex complexity and participation approximately follows a power- law.
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Additional File 4:
Mammalian complex complexity and protein length. The mean length of proteins in available mammalian complexes is examined with respect to complex complexity.
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Additional File 5:
Median length of proteins in annotated human complexes. The median length of proteins in human complexes is examined with respect to complex complexity.
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Additional File 6:
Yeast complex complexity and protein length. The mean length of proteins in available yeast complexes is examined with respect to complex complexity.
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Additional File 7:
Length distribution of human mitochondrial proteins. The length distribution of human mitochondrial proteins is plotted.
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Additional File 8:
Random complexes and dN/dS (Human-Mouse Orthologs). dN/dS ratios of genes associated with model 2 random complexes are examined with respect to complex complexity and participation.
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Additional File 9:
Binned Plots for Figures 3D and 3F.3
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Additional File 10:
Protein complexes and dN/dS based on orthologs from a variety of species. dN/dS ratios of genes based on human-dog, human-chimp, human-rat, S. cerevisiae-S. mikatae and S. cerevisiae-S. paradoxus orthologs are examined with respect to complex complexity and participation.
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Additional File 11:
Complexes and gene conservation. The fraction of orthologs conserved in yeast and human complexes is examined against complex complexity.
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Additional File 12:
Extension and subsets of the protein complex data. Extended yeast complexes, complexes with subcomplexes removed, nuclear and non-nuclear complexes are examined with respect to complex complexity and participation.
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Additional File 13:
Analysis of protein complex data using the median. Analysis of protein complex data with respect to mean dN/dS ratios and sequence length is compared with analysis using the median.
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Additional File 14:
Homogeneity of Protein Properties in Yeast Complexes. Deviation in pI, secondary structure and evolutionary rate between proteins in annotated yeast complexes are compared to those in random complexes.
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Additional File 15:
Length difference of interacting proteins. Large proteins tend to interact with much smaller partners.
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