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J. Cell Sci. 117 (13): 2769-2775

Role of the cytoskeleton in signaling networks

Gabor Forgacs1,*, Soon Hyung Yook2, Paul A. Janmey3, Hawoong Jeong2,4, and Christopher G. Burd5

1 Department of Physics and Biology, University of Missouri, Columbia, MO 65211, USA
2 Department of Physics, Notre Dame University, Notre Dame, IN 46556, USA
3 Institute for Medicine and Engineering, Department of Physiology, University of Pennsylvania School of Medicine, 3340 Smith Walk, Philadelphia, PA 19104, USA
4 Department of Physics, Korea Advanced Institute of Science and Technology, Taejon, 305-701, Korea
5 Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, 421 Curie Boulevard, Philadelphia, PA 19104, USA



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Fig. 1. The largest connected cluster of 1458 interacting proteins of the database by Uetz et al. (Uetz et al., 2000Go). In this cluster, yellow and green dots denote cytoskeletal and signaling proteins, respectively, as defined by our criteria. Proteins in red are shared by the two subclasses. The analogous cluster in the D network contains 4198 proteins. It is not shown here because the density of proteins was too high for visual examination.

 


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Fig. 2. Distance distribution P(d) for proteins in the various classes. The notations in the figure are as follows: c-c, cytoskeleton-cytoskeleton; s-s, signaling-signaling; c-s, signaling-cytoskeleton. P(d) for all proteins includes distances between any two proteins. Numbers in brackets give the average distances (<d>) between indicated proteins. (a) Results based on the database of Uetz et al. (Uetz et al., 2000Go). (b) Results based on the DIP database. The larger number of proteins in the DIP dataset is manifest in a narrower distance distribution and higher peak values.

 


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Fig. 3. Plot of the rescaled average local clustering index <md>/<mrand> using the database of Uetz et al. (Uetz et al., 2000Go) (left) and the DIP database (right).

 


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Fig. 4. The nearest-neighbor clustering index <m1(x/y)>. Arrows point from x to y. Left half in a and b U database and DIP database, respectively, summarize results from Fig. 3. Right half present results for pseudo protein classes that were constructed by randomly selecting 74 (U) and 92 (D) pseudo c class proteins, and 141(U) and 207 (D) pseudo s class proteins from the fully connected clusters.

 


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Fig. 5. <md(s/i)>/mrand (i=0 to14) for fifteen functional protein classes in addition to the s and c classes. Plots are based on the database by Uetz et al. (Uetz et al., 2000Go) (top) and the DIP database (bottom). The 15 functional protein classes are: 0, metabolism; 1, energy; 2, cell growth, cell division and DNA synthesis; 3, transcription; 4, protein synthesis; 5, protein destination; 6, transport facilitation; 7, cellular transport and transport mechanisms; 8, cellular biogenesis; 9, cell rescue, defence, cell death and ageing; 10, ionic homeostasis; 11, cellular organization; 12, transposable elements; viral and plasmid proteins; 13, classification not yet clear cut; 14, unclassified proteins.

 


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Fig. 6. <md(c/i)>/mrand (i=0 to14) for 15 functional protein classes in addition to the s and c classes. Plots are based on the database by Uetz et al. (Uetz et al., 2000Go) (top) and the DIP database (bottom). The fifteen protein classes are the same as in Fig. 5.

 


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Fig. 7. Combined c-s signaling subnetwork, derived from the largest connected cluster in Fig. 1. Yellow and green dots denote signaling and cytoskeletal proteins, respectively, proteins in red are shared by the two subclasses. Only proteins with at least one connection are shown. [Results are only shown for the database by Uetz et al. (Uetz et al., 2000Go).]

 


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Fig. 8. The signaling subnetwork shown in Fig. 7, after the s proteins that connect to the cytoskeleton were taken out. [Results are only shown for the database by Uetz et al. (Uetz et al., 2000Go).]

 


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