Topology of mammalian transcription networks.
We present a first attempt to evaluate the generic topological principles underlying the mammalian transcriptional regulatory networks. Transcription networks, TN, studied here are represented as graphs where vertices are genes coding for transcription factors and edges are causal links between the genes, each edge combining both gene expression and trans-regulation events. Two transcription networks were retrieved from the TRANSPATH database: The first one, TN_RN, is a 'complete' transcription network referred to as a reference network. The second one, TN_p53, displays a particular transcriptional sub-network centered at p53 gene. We found these networks to be fundamentally non-random and inhomogeneous. Their topology follows a power-law degree distribution and is best described by the scale-free model. Shortest-path-length distribution and the average clustering coefficient indicate a small-world feature of these networks. The networks show the dependence of the clustering coefficient on the degree of a vertex, thereby indicating the presence of hierarchical modularity. Clear positive correlation between the values of betweenness and the degree of vertices has been observed in both networks. The top list of genes displaying high degree and high betweennes, such as p53, c-fos, c-jun and c-myc, is enriched with genes that are known as having tumor-suppressor or proto-oncogene properties, which supports the biological significance of the identified key topological elements.
Potapov
Anatolij P
AP
Department of Bioinformatics, UKG, University of Göttingen, Goldschmidtstrasse 1, D-37077 Göttingen, Germany. apo@bioinf.med.uni-goettingen.de
Voss
Nico
N
Sasse
Nicole
N
Wingender
Edgar
E
D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D008322:Mammals / Q000235:genetics* / Q000378:metabolism; D000090063:Proto-Oncogene Mas; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics*; D014158:Transcription, Genetic
C000715470:MAS1 protein, human; D000090063:Proto-Oncogene Mas; D014157:Transcription Factors