53,838 research outputs found
Game Theory applied to gene expression analysis.
This is a summary of the authorâs Ph.D. thesis supervised by Fioravante Patrone and Stefano Bonassi and defended on 25 May 2006 at the UniversitĂ degli Studi di Genova. The thesis in written in English and a copy is available from the author upon request. This work deals with the discussion and the application of a methodology based on Game Theory for the analysis of gene expression data. Nowadays, microarray technology is available for taking âpicturesâ of gene expressions. Within a single experiment of this sophisticated technology, the level of expression of thousands of genes can be estimated in a sample of cells under given conditions. Roughly speaking, the starting point is the observation of a âpictureâ of gene expressions in a sample of cells under a biological condition of interest, for example a tumor. Then, Game Theory plays a primary role to quantitatively evaluate the relevance of each gene in regulating or provoking the condition of interest, taking into account the observed relationships in all subgroups of genes.Coalitional game; Shapley value; Power index; Gene expression; Microarray;
Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution
<p>Abstract</p> <p>Background</p> <p>In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low <it>p</it>-value. However, the interpretation of each single <it>p</it>-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, <it>game theory </it>has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions.</p> <p>Results</p> <p>In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called <it>Comparative Analysis of Shapley value </it>(shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability.</p> <p>Conclusion</p> <p>CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways.</p
Identification of low intratumoral gene expression heterogeneity in neuroblastic tumors by genome-wide expression analysis and Game Theory
BACKGROUND. Neuroblastic tumors (NTs) are largely comprised of neuroblastic (Nb) cells with various quantities of Schwannian stromal (SS) cells. NTs show a variable genetic heterogeneity. NT gene expression profiles reported so far have not taken into account the cellular components. The authors reported the genome-wide expression analysis of whole Minors and microdissected Nb and SS cells. METHODS. The authors analyzed gene expression profiles of 10 stroma-poor NTs (NTs-SP) and 9 stroma-rich NTs (NTS-SR) by microarray technology. Nb and SS cells were. isolated by laser microdissection from NTs-SP and NTs-SR and probed with microarrays. Gene expression data were analyzed by the Significance Analysis of Microarrays (SAM) and Game Theory (GT) methods, the latter applied for the first time to microarray data evaluation. RESULTS. SAM identified 84 genes differentially expressed between NTs-SP and NTs-SR, whereas 50 were found by GT. NTs-SP mainly express genes associated with cell replication, nervous system development, and antiapoptotic pathways, whereas NTs-SR express genes of cell-cell communication and apoptosis. Combining SAM and GT, the authors found 16 common genes driving the separation between NTs-SP and NTs-SR. Five genes overexpressed in NTs-SP encode for nuclear proteins (CENPE, EYA1, PBK TOP2A, TFAP2B), whereas only 1 of 11 highly expressed genes in NTs-SR encodes for a nuclear receptor (NR4A2). CONCLUSIONS. The results showed that NT-SP and NT-SR gene signatures differ for a set of genes involved in distinct pathways, and the authors demonstrated a low intratumoral heterogeneity at the mRNA level in both NTs-SP and NTs-SR. The combination of SAM and GT methods may help to better identify gene expression profiling in NTs
Attribute Exploration of Discrete Temporal Transitions
Discrete temporal transitions occur in a variety of domains, but this work is
mainly motivated by applications in molecular biology: explaining and analyzing
observed transcriptome and proteome time series by literature and database
knowledge. The starting point of a formal concept analysis model is presented.
The objects of a formal context are states of the interesting entities, and the
attributes are the variable properties defining the current state (e.g.
observed presence or absence of proteins). Temporal transitions assign a
relation to the objects, defined by deterministic or non-deterministic
transition rules between sets of pre- and postconditions. This relation can be
generalized to its transitive closure, i.e. states are related if one results
from the other by a transition sequence of arbitrary length. The focus of the
work is the adaptation of the attribute exploration algorithm to such a
relational context, so that questions concerning temporal dependencies can be
asked during the exploration process and be answered from the computed stem
base. Results are given for the abstract example of a game and a small gene
regulatory network relevant to a biomedical question.Comment: Only the email address and reference have been replace
Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better
Joel Cohen offers a historical and prospective analysis of the relationship between mathematics and biolog
The Dynamics of Sex Ratio Evolution: From the Gene Perspective to Multilevel Selection
The new dynamical game theoretic model of sex ratio evolution emphasizes the
role of males as passive carriers of sex ratio genes. This shows inconsistency
between population genetic models of sex ratio evolution and classical
strategic models. In this work a novel technique of change of coordinates will
be applied to the new model. This will reveal new aspects of the modelled
phenomenon which cannot be shown or proven in the original formulation. The
underlying goal is to describe the dynamics of selection of particular genes in
the entire population, instead of in the same sex subpopulation, as in the
previous paper and earlier population genetics approaches. This allows for
analytical derivation of the unbiased strategic model from the model with
rigorous non-simplified genetics. In effect, an alternative system of
replicator equations is derived. It contains two subsystems: the first
describes changes in gene frequencies (this is an alternative unbiased
formalization of the Fisher-Dusing argument), whereas the second describes
changes in the sex ratios in subpopulations of carriers of genes for each
strategy. An intriguing analytical result of this work is that fitness of a
gene depends on the current sex ratio in the subpopulation of its carriers, not
on the encoded individual strategy. Thus, the argument of the gene fitness
function is not constant but is determined by the trajectory of the sex ratio
among carriers of that gene. This aspect of the modelled phenomenon cannot be
revealed by the static analysis. Dynamics of the sex ratio among gene carriers
is driven by a dynamic "tug of war" between female carriers expressing the
encoded strategic trait value and random partners of male carriers expressing
the average population strategy (a primary sex ratio). This mechanism can be
called "double level selection". Therefore, gene interest perspective leads to
multi-level selection.Comment: 3 figure
Data based identification and prediction of nonlinear and complex dynamical systems
We thank Dr. R. Yang (formerly at ASU), Dr. R.-Q. Su (formerly at ASU), and Mr. Zhesi Shen for their contributions to a number of original papers on which this Review is partly based. This work was supported by ARO under Grant No. W911NF-14-1-0504. W.-X. Wang was also supported by NSFC under Grants No. 61573064 and No. 61074116, as well as by the Fundamental Research Funds for the Central Universities, Beijing Nova Programme.Peer reviewedPostprin
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