Applied Statistics for Network Biology: Methods in Systems by Matthias Dehmer, Frank Emmert-Streib, Armin Graber, Armindo

By Matthias Dehmer, Frank Emmert-Streib, Armin Graber, Armindo Salvador

This publication introduces a few innovative statistical equipment that are used for the research of genomic, proteomic and metabolomic facts units. particularly within the box of platforms biology, researchers try to research as much facts as attainable in a given organic process (such as a mobilephone or an organ). the correct statistical evaluate of those huge scale facts is important for the proper interpretation and various experimental techniques require assorted ways for the statistical research of those information. This booklet is written by way of biostatisticians and mathematicians yet aimed toward experimental researcher in addition to computational biologists who usually lack a suitable history in statistical research.

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3 Network Motifs Compared with the former two measurements, which could be applied to any kinds of networks, network motifs are usually employed in directed networks, such as transcriptional regulatory networks or transcription factor target networks. Network motifs could be regarded as the basic blocks to form the whole network [13], and they were shown to be important in maintaining robustness, perturbation buffering, quick responses, and accurate signal transductions [13–15]. Thus, the genes that take part in multiple network motifs should be more important and counting network motifs becomes one measurement for evaluating the importance of genes.

2 discusses numerical methods for simulating chemical reaction systems. These methods are the theoretical basis for designing stochastic models in the following sections. 3. 4 provides a number of techniques for designing continuous stochastic models by using SDEs. 2 Discrete Stochastic Simulation Methods Since many cellular processes are governed by effects associated with small numbers of certain key molecules, the standard chemical framework described by systems of ODEs breaks down. The stochastic simulation algorithm (SSA) represents a discrete modeling approach and an essentially exact procedure for numerically simulating the time evolution of a well-stirred reaction system [39].

Rather than studying the pathway with all the 40 binding configurations, the proposed system included only a number of major binding configurations and nonspecific binding was ignored. Bifurcation analysis demonstrated that the proposed model for a system with three binding sites (OR1, OR2, and OR3) had a much larger bistable region than a mutant system with only two binding sites (OR2 and OR3) [35]. Based on the model for the system with three binding sites, external noise was introduced into the deterministic model to study the influence of environmental fluctuations on the system bistability.

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