reconstruction of gene regulatory networks

... modeling of gene regulatory networks in, for example, [25,26] Furthermore, methods for inferring PBN have been developed in [27] One disadvantage of Boolean models for gene regulatory networks ... d’Alche-Buc, Gene networks inference using dynamic Bayesian networks, Bioinformatics 19, 138–148 (2003) 10 N Radde, L Kaderali, Bayesian Inference of Gene Regulatory Networks Using Gene Expression ... be generated However, this comes at the expense of having to compute the entire Gröbner fan of the ideal of points For small networks the computation of the fan is feasible but as the number of...

Ngày tải lên: 21/06/2014, 03:20

... exists a gene among its regulatory set such that if the gene takes on a certain value, then that value determines the value of the function irrespective of the values of the other regulatory genes ... from which the random networks are to be generated While it might first appear that one should generate networks using the class Gg composed of all Boolean networks containing g genes, this is not ... model cost of 2di + 2d f + To show the effect of the encoding scheme we generated one hundred 6 -gene networks, each of which was observed over 50 time points Λ and F were fixed so that one gene would...

Ngày tải lên: 21/06/2014, 22:20

... Wierling, H Lehrach, and R Herwig, Reconstruction and validation of gene regulatory networks with neural networks, ” in Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference ... individual, gene- dependent regulation strengths {ati } of each transcription factor ti ∈ T of the gene, we derived the kinetic law: results For this study we generated randomly five networks of sizes ... the impact of missing data on the reconstruction results, since in real experiments there are often not all genes included in the dataset It is shown that the reliable reconstruction of the whole...

Ngày tải lên: 22/06/2014, 00:20

... concentrations of mRNA and proteins induced by gene i, respectively, ci (t) is the fraction of DNA fragments committed to transcription of gene i, κi is the transcription rate of gene i, and τ ... transcriptional regulatory system (tRS) We generate networks using this model and a fixed set θ of parameters We call these networks reference networks A reference network is identified by its set θ of parameters, ... straightforward simulation consists of the design of a reference network, the design of a projected network (for some value of Δx ), the generation of several trajectories for both networks from randomly...

Ngày tải lên: 22/06/2014, 19:20

... Construction of Gene Regulatory Networks using biclustering and Bayesian networks Fadhl M Alakwaa1*§, Nahed H Solouma and Yasser M Kadah3* University of Science and Technology, Sana'a, Yemen Department of ... number of sophisticated approaches to the reverse engineering of cellular networks from gene expression data have emerged These include Boolean networks [3], Bayesian networks [4], association networks ... differential equations [7] The reconstruction of gene networks is in general complicated by the high dimensionality of high-throughput data; i.e a dataset consists of relatively few time points...

Ngày tải lên: 13/08/2014, 16:20

... dimensionality of the microarray data and display the overall separation of samples from autistic and control groups Prediction of the potential target genes The lists of the potential target genes of the ... findings of our gene expression analyses [21,40,77] Significantly, we verify inverse changes in the levels of putative target genes of two of the altered brainspecific miRNAs through the use of anti-miRs ... diagnosis of autism and unrelated autistic case-controls reveal the differential expression of hundreds to thousands of genes [21,40,77], suggesting that higher level epigenetic gene regulatory...

Ngày tải lên: 11/08/2014, 12:20

... later Two classes of functions that may be reasonable models of functions in genetic regulatory networks are presented For both of these classes, it is assumed that the number of essential variables ... elucidates bacterial networks Nature 429(6987), 9296 (2004) doi:10.1038/nature02456 10 S Schober, K Mir, M Bossert, Reconstruction of boolean genetic regulatory networks consisting of canalyzing or ... then k, where k is the number of controlling variables for a function Further the class of 1-low networks, which include unate networks, linear threshold networks, and networks with nested canalyzing...

Ngày tải lên: 20/06/2014, 22:20

... level of gene i is the result of linear combination of the expression levels of the regulating genes at previous sample time To make further simplification, we assume the regulation is a time-homogeneous ... estimates of the networks and are considered as “hard” solutions The advantage of soft solutions has been demonstrated in digital communications [20] In the context of GRNs, the APPs from the soft ... learning the structure of the DBNs In specific, if we can determine that genes and are the parents of gene in the DBNs, there will be directed links going from gene and to gene in the uncovered...

Ngày tải lên: 22/06/2014, 19:20

... draft of the sea urchin genome sequence verifies that the established gene catalog contains a tag for more than 50% of all sea urchin genes Out of a total of 28,944 predicted sea urchin gene refereed ... Figure Coexpression of genes in SMC cells Coexpression of genes in SMC cells Whole-mount in situ hybridization (WISH) analysis of examples of signaling and transcription factor genes identified ... 40 cycles of 95°C for 15 s and 60°C for To determine the expression of a specific gene, SpZ12-1 amplification for normalizing measurements of the absolute number of transcripts of the gene as well...

Ngày tải lên: 14/08/2014, 07:21

... direction of change) between the Hughes et al swi4∆ profile and our new profile Expression changes were reproducible for 28 of 42 Msn4p-regulated genes, 11 of 29 Hap4p-regulated genes, and 64 of 119 ... given by: The expression coherence of a set of genes measures whether the expression levels of these genes behave similarly in a particular experiment Each gene i in gene- deletion experiment e has ... automated design of new experiments First, we use the previously described modeling procedure to generate a library of models corresponding to different gene- regulatory systems in yeast Many of these...

Ngày tải lên: 14/08/2014, 14:21

... of Pax1 and Pax9 mouse lines for TF mapping studies……….87   vi   3.5 Gene expression profiling profiling - Pax1 and Pax9 targets in the vertebral column……….91 3.5.1 Gene expression profile of ... by differential gene expression Such spatio-temporally regulated expression of a combination of genes, is called the gene battery” [3, 10] As a single gene can have multiple cis -regulatory elements ... experimenting on two of the genes, Pax1 and Pax9 The objective of this study is to identify the target genes of Pax1 and Pax9 in the IVD, using traditional gene- targeting strategies (loss -of- function...

Ngày tải lên: 08/09/2015, 21:57

... (Chapter 7) a) detection of new co-regulated genes, and b) deciphering parts of gene networks of which AMP genes are members 1.4 Contribution of this thesis AMP-coding genes and their products ... unfolding of possible new association of genes with other genes (in terms of co-regulation) of the same pathway and unearthing parts and functions of the underlying gene networks which earlier have not ... regions of the human genome and determining parts of potential transcription regulatory networks in which some of the AMP genes are possibly involved 5) Providing a functional analysis of the genes...

Ngày tải lên: 14/09/2015, 09:05

... specific genes are expressed (Davidson E.H.2006) These inter-regulating genes form the gene regulatory networks that control development There are some general features of Gene Regulatory Networks: ... factors and the cis -regulatory elements that read the regulatory state of a cell that form the Gene Regulatory Networks (GRNs) which control development Studying gene regulatory networks involves ... The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, 2006 The whole process of development of an embryo can be viewed as dynamic progression through a series of regulatory...

Ngày tải lên: 04/10/2015, 16:03

... (University of Indiana, Bloomington, IN, USA) [23] This vector carries the regulatory region of the b2-tubulin gene driving testis-specific expression of any gene substituting the b2-tubulin ORF The regulatory ... the upregulation of expression of a single b subunit gene, the fruit fly has generated in evolution two specialized genes for this purpose Despite the accumulation of large amount of information ... functions of the CK2 b subunits in higher eukaryotes is still open We tried to address this issue on the model of spermatogenesis in Drosophila by making a Ôknock-downÕ of the CK2btes gene by means of...

Ngày tải lên: 21/02/2014, 15:20

... melted DNA Generation of a DNA atlas for each of the two contigs covering the CFTR gene (ac000111 and ac000061) enabled the prediction of DNase sensitivity and YR steps that predict ease of melting ... temporal regulation of the CFTR gene predicts that co-operation of many different regulatory elements may contribute to CFTR expression in the chromatin environment in vivo DHS are often, though not ... detect One disadvantage of analysing carcinoma cell lines is that some of the DHS we observe may be the result of these lines showing aberrant gene expression following tumorigenesis, rather than...

Ngày tải lên: 08/03/2014, 10:20

... constituent of membrane, we examined whether glutamine regulates the expression of genes involved in cholesterol homeostasis To investigate the effect of glutamine on the transcription of genes related ... in the induction of SREBP-1a gene expression When endogenous Sp1 expression was reduced to  20% of normal with gene- specific small interfering RNA (siRNA), the gene expression of SREBP-1a was ... of SREBP functions The most likely are, first, an increase in the gene expression of SREBPs, and second, the enhancement of SREBP processing by glutamine We therefore investigated the effect of...

Ngày tải lên: 28/03/2014, 22:21

... part of a target gene, it can be referred to either by the name of this gene or by the name of the regulator protein that binds to it It is thus necessary to discriminate between “binding site of ... of a gene is a challenging problem as this fact can be expressed in a variety of ways—possibly mentioning neither the biological process (expression) nor any of the two biological entities (genes ... chunks relevant for the gene transcription domain, e.g [nxgene The GAL4 gene ] Relation chunking Relations between entities are recognized, e.g The expression of the cytochrome genes CYC1 and CYC7...

Ngày tải lên: 31/03/2014, 03:20

... for the reconstruction of potential attack scenarios in the context of MASNet, is of major importance To the best of our knowledge, none of the existing research has considered the problem of formal ... MASNets [9] To the best of our knowledge, none of the existing research has considered the problem of formal investigation of digital security attacks in the context of wireless networks In this article ... support the generation of irrefutable proofs regarding reconstructed attack scenarios, reducing the complexity of their generation, and automating the reasoning on incidents A review of these approaches,...

Ngày tải lên: 21/06/2014, 02:20

... size of regulatory networks Our study aims in the same direction of investigating system properties of a new synthesis of the population genetics of development, using explicit modeling of the ... population and quantitative genetics of evolving Boolean regulatory networks, and evaluated the performance as well as the effects of mutations in regulatory networks of different connectivity, while ... most of the higher levels of environmental heterogeneity (u) Discussion In our conceptual simulation study we have investigated the relation of a specific structural parameter of regulatory networks, ...

Ngày tải lên: 22/06/2014, 00:20

... sRogers generator produces the topology of the genetic network according to an approximate power-law distribution on the number of regulatory connections out of each gene The normal steady state of ... a set of benchmarks on the basis of artificially generated microarray datasets In spite of the evident limitations of using synthetic data, this makes possible a quantitative assessment of the ... using relevance networks, ” Proceedings of the National Academy of Sciences of the United States of America, vol 97, no 22, pp 12182–12186, 2000 [16] T M Cover and J A Thomas, Elements of Information...

Ngày tải lên: 22/06/2014, 19:20