Computational Methods in Systems Biology
Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-β Signaling Jean C ...
92 J. Coquet et al. 1 Introduction Living cells use molecular signaling networks to adapt their phenotype to the microenvironmen ...
Identifying Functional Families of Trajectories 93 that includes canonical and non-Smad pathways [ 2 ]. Using this model they id ...
94 J. Coquet et al. Fig. 1.Example of the generation of trajectories from PID maps and their pre- processing. (A) The signaling ...
Identifying Functional Families of Trajectories 95 Q(t)function for ranking the trajectories by decreasing correlation tot.A tra ...
96 J. Coquet et al. Table 3.Example of partial ordering of all trajectories for every trajectoryti.All trajectories are sorted f ...
Identifying Functional Families of Trajectories 97 For studying the RSC clustering robustness, we performed 64 (= 4× 4 ×4) analy ...
98 J. Coquet et al. Fig. 2.Example of calculation for determining over-represented proteins between three coresoftrajectories.(A ...
Identifying Functional Families of Trajectories 99 Fig. 3.Distribution of (A) the number of molecules for each trajectory and (B ...
100 J. Coquet et al. Fig. 4.Hierarchical classification of the clusters generated by the 320 clusterings using varying parameter ...
Identifying Functional Families of Trajectories 101 Table 4.Statistics of clusters. Group 1 Group 2 Group 3 Group 4 Group 5 Numb ...
102 J. Coquet et al. Based on the scores of proteins over-representation in trajectories, we next searched for the biological si ...
Identifying Functional Families of Trajectories 103 Fig. 7.Screenshot of the Web visualization of core 1. A node is a bio-molecu ...
104 J. Coquet et al. 4 Discussion Cell signaling networks are essential to life. They allow cells to sense and inter- pret micro ...
Identifying Functional Families of Trajectories 105 whereas the lowest and highest values ofx 2 were associated to group 3. This ...
106 J. Coquet et al. Bierie, B., Moses, H.L.: Tumour microenvironment: TGFβ: the molecular Jekyll andHydeofcancer.Nat.Rev.Cance ...
Identifying Functional Families of Trajectories 107 Tian, M., Neil, J.R., Schiemann, W.P.: Transforming growth factor-βand the ...
Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs Fran ̧cois ...
Strong Turing Completeness 109 always been shown to be encodable in Turing machines. The more recent phys- ical Church-Turing th ...
110 F. Fages et al. We first show the Turing completeness in the strong sense of uniform com- putability, of elementary biochemi ...
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