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Register a new userThe topology of the transcription regulatory network in the yeast, S. cerevisiae
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MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the genetic network of a cell or microorganism. Experimental manipulation of gene activity coupled with the assessment of perturbed transcriptome (i. e., global mRNA expression) patterns represents one approach toward this goal, and may provide a backbone into which other measurements can be later integrated. RESULT: We use microarray data on 287 single gene deletion Saccharomyces cerevisiae mutant strains to elucidate generic relationships among perturbed transcriptomes. Their comparison with a method that preferentially recognizes distinct expression subpatterns allows us to pair those transcriptomes that share localized similarities. Analyses of the resulting transcriptome similarity network identify a continuum hierarchy among the deleted genes, and in the frequency of local similarities that establishes the links among their reorganized transcriptomes. We also find a combinatorial utilization of shared expression subpatterns within individual links, with increasing quantitative similarity among those that connect transcriptome states induced by the deletion of functionally related gene products. This suggests a distinct hierarchical and combinatorial organization of the S. cerevisiae transcriptional activity, and may represent a pattern that is generic to the transcriptional organization of all eukaryotic organisms. AVAILABILITY: Detailed analyses of the comparison method and free software are available from the authors and at http://angel.elte.hu/bioinf
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Time-series of high throughput gene sequencing data intended for gene regulatory network (GRN) inference are often short due to the high costs of sampling cell systems. Moreover, experimentalists lack a set of quantitative guidelines that prescribe the minimal number of samples required to infer a reliable GRN model. We study the temporal resolution of data vs quality of GRN inference in order to ultimately overcome this deficit. The evolution of a Markovian jump process model for the Ras/cAMP/PKA pathway of proteins and metabolites in the G1 phase of the Saccharomyces cerevisiae cell cycle is sampled at a number of different rates. For each time-series we infer a linear regression model of the GRN using the LASSO method. The inferred network topology is evaluated in terms of the area under the precision-recall curve AUPR. By plotting the AUPR against the number of samples, we show that the trade-off has a, roughly speaking, sigmoid shape. An optimal number of samples corresponds to values on the ridge of the sigmoid.
Gene transcription is a stochastic process mostly occurring in bursts. Regulation of transcription arises from the interaction of transcription factors (TFs) with the promoter of the gene. The TFs, such as activators and repressors can interact with the promoter in a competitive or non-competitive way. Some experimental observations suggest that the mean expression and noise strength can be regulated at the transcription level. A Few theories are developed based on these experimental observations. Here we re-establish that experimental results with the help of our exact analytical calculations for a stochastic model with non-competitive transcriptional regulatory architecture and find out some properties of Noise strength (like sub-Poissonian fano factor) and mean expression as we found in a two state model earlier. Along with those aforesaid properties we also observe some anomalous characteristics in noise strength of mRNA and in variance of protein at lower activator concentrations.
We demonstrate that with appropriate quantum correlation function, a real-space network model can be constructed to study the phase transitions in quantum systems. For the three-dimensional bosonic system, the single-particle density matrix is adopted to construct the adjacency matrix. We show that the Bose-Einstein condensate transition can be interpreted as the transition into a small-world network, which is accurately captured by the small-world coefficient. For the one-dimensional disordered system, using the electron diffusion operator to build the adjacency matrix, we find that the Anderson localized states create many weakly-linked subgraphs, which significantly reduces the clustering coefficient and lengthens the shortest path. We show that the crossover from delocalized to localized regimes as a function of the disorder strength can be identified as the loss of global connection, which is revealed by the small-world coefficient as well as other independent measures like the robustness, the efficiency, and the algebraic connectivity. Our results suggest that the quantum phase transitions can be visualized in real space and characterized by the network analysis with suitable choices of quantum correlation functions.
The Topological Hypothesis states that phase transitions should be related to changes in the topology of configuration space. The necessity of such changes has already been demonstrated. We characterize exactly the topology of the configuration space of the short range Berlin-Kac spherical model, for spins lying in hypercubic lattices of dimension d. We find a continuum of changes in the topology and also a finite number of discontinuities in some topological functions. We show however that these discontinuities do not coincide with the phase transitions which happen for d >= 3, and conversely, that no topological discontinuity can be associated to them. This is the first short range, confining potential for which the existence of special topological changes are shown not to be sufficient to infer the occurrence of a phase transition.
We study the dynamics of networks with coupling delay, from which the connectivity changes over time. The synchronization properties are shown to depend on the interplay of three time scales: the internal time scale of the dynamics, the coupling delay along the network links and time scale at which the topology changes. Concentrating on a linearized model, we develop an analytical theory for the stability of a synchronized solution. In two limit cases the system can be reduced to an effective topology: In the fast switching approximation, when the network fluctuations are much faster than the internal time scale and the coupling delay, the effective network topology is the arithmetic mean over the different topologies. In the slow network limit, when the network fluctuation time scale is equal to the coupling delay, the effective adjacency matrix is the geometric mean over the adjacency matrices of the different topologies. In the intermediate regime the system shows a sensitive dependence on the ratio of time scales, and specific topologies, reproduced as well by numerical simulations. Our results are shown to describe the synchronization properties of fluctuating networks of delay-coupled chaotic maps.
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