An evolutionary and structural characterization of mammalian protein complex organization

doi:10.1186/1471-2164-9-629

BMC Genomics

Volume 9

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Wong P
Althammer S
Hildebrand A
Kirschner A
Pagel P
Geissler B
Smialowski P
Blöchl F
Oesterheld M
Schmidt T
Strack N
Theis FJ
Ruepp A
Frishman D

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Wong P
Althammer S
Hildebrand A
Kirschner A
Pagel P
Geissler B
Smialowski P
Blöchl F
Oesterheld M
Schmidt T
Strack N
Theis FJ
Ruepp A
Frishman D
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Research article

An evolutionary and structural characterization of mammalian protein complex organization

Philip Wong¹ , Sonja Althammer¹^* , Andrea Hildebrand¹^* , Andreas Kirschner²^* , Philipp Pagel¹^,2^* , Bernd Geissler² , Pawel Smialowski¹^,2 , Florian Blöchl¹ , Matthias Oesterheld¹ , Thorsten Schmidt¹^,2 , Normann Strack¹ , Fabian J Theis¹^,3 , Andreas Ruepp¹ and Dmitrij Frishman¹^,2

¹Helmholtz Center Munich – German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1 D-85764 Neuherberg, Germany

²Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, 85350 Freising, Germany

³Max-Planck-Institute for Dynamics and Self-Organization, Bunsenstrasse 10, 37073 Göttingen, Germany

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:629doi:10.1186/1471-2164-9-629


Published:	23 December 2008

Additional 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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