using eqtls to reconstruct gene regulatory networks

... biology is to reveal how genes and their products interact to regulate cellular process To achieve this goal it is necessary to reconstruct gene regulatory networks (GRN), which help us to understand ... development, gene regulatory networks (GRNs) have to be constructed During the last decade, many GRN inference algorithms based on genome-wide data have been developed to unravel the complexity of gene ... patterns Genes whose transcription is responsive to a variety of stresses have been implicated in a general Yeast response to stress (awkward) Other gene expression responses appear to be specific to...

Ngày tải lên: 13/08/2014, 16:20

... However, a lot more needs to be known in terms of the regulatory mechanisms of AMPs To understand the regulatory mechanism of AMPs or any other genes, the identification of regulatory elements is the ... transcription regulatory networks in which some of the AMP genes are possibly involved 5) Providing a functional analysis of the genes so identified and their relation to particular gene networks ... AMP genes be found using the non-homology, promoter analysis based approach? This thesis has attempted to answer these questions by using examples of several AMP gene families To be able to address...

Ngày tải lên: 14/09/2015, 09:05

... form the Gene Regulatory Networks (GRNs) which control development Studying gene regulatory networks involves the identification of the transcription factors expressed and the cis -regulatory elements ... inter-regulating genes form the gene regulatory networks that control development There are some general features of Gene Regulatory Networks: 1) It is the specific combination of transcription factors present ... different time points are obtained, it is important to reconstruct the gene regulatory network Several mathematical formalisms for modeling gene regulatory networks from expression data are available...

Ngày tải lên: 04/10/2015, 16:03

... 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 ... as well as the gene dependencies, in biochemical regulatory networks from experimental data The algorithm can handle large regulatory networks and hence is applicable to many networks of interest ... qualitative relations in genetic networks and metabolic path-ways Bioinformatics 16(8), 727–734 (2000) T Tian, K Burrage, Stochastic models for regulatory networks of the genetic toggle switch, PNAS...

Ngày tải lên: 21/06/2014, 03:20

... approach to constructing probabilistic gene regulatory networks, ” Bioinformatics, vol 20, no 17, pp 2918–2927, 2004 [10] W Zhao, E Serpedin, and E R Dougherty, “Inferring gene regulatory networks ... 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 ... requires that we store this structure parameter as well The simplest ways to accomplish this are by using g (the total number of genes) bits as indicators or by using log g bits to represent the...

Ngày tải lên: 21/06/2014, 22:20

... input genes, which have no regulatory elements in the model and regulated genes, which have at least one regulator Input genes have a constant linear production In contrast, regulated genes have ... Falciani, Z Ghahramani, C Rangel, and D L Wild, “A Bayesian approach to reconstructing genetic regulatory networks with hidden factors,” Bioinformatics, vol 21, no 3, pp 349–356, 2005 [12] N Friedman, ... approach of using simulated data and presented a framework for testing microarray data analysis tools An artificial data generator has to be independent of the reverse engineering algorithms to avoid...

Ngày tải lên: 22/06/2014, 00:20

... Bayesian networks to discover genetic regulatory networks, ” Simulation, vol 79, no 12, pp 689–702, 2003 [16] M J Beal, F Falciani, Z Ghahramani, C Rangel, and D L Wild, “A Bayesian approach to reconstructing ... uncovering the underlying gene regulatory networks This is equivalent to learning the structure of the DBNs In specific, if we can determine that genes and are the parents of gene in the DBNs, there ... reconstructing genetic regulatory networks with hidden factors,” Bioinformatics, vol 21, no 3, pp 349–356, 2005 [17] B.-E Perrin, L Ralaivola, A Mazurie, S Bottani, J Mallet, and F d’Alch´ -Buc, Gene networks...

Ngày tải lên: 22/06/2014, 19:20

... network is used to generate gene expression data, which is then used to reconstruct the network [15] A key drawback of most approaches is that the comparison is applicable only to networks with ... called a (discrete) 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 ... Point Trajectories Steady-State trajectories Trajectory Transient part of the trajectory Steady-state part of the trajectory Cumulative distribution functions Distance between two trajectories Distance...

Ngày tải lên: 22/06/2014, 19:20

... of genes [21,40,77], suggesting that higher level epigenetic gene regulatory mechanisms are involved in ASD The present study provides further insight into the post-transcriptional gene regulatory ... expression level cutoff of log2(ratio) ≥ ±0.4 was applied to the differentially expressed genes, which reduced the list of potential gene targets to 94 genes IPA analysis of this set of genes (Table ... differentially expressed genes was inversely correlated with that of the respective potentially regulatory miRNAs Relational gene networks constructed using computational network prediction tools show that...

Ngày tải lên: 11/08/2014, 12:20

... The artificial data involves regulators (R1, R2) and genes (G1–G9) Names Regulator R1 Regulator R2 Gene G1 Gene G2 Gene G3 Gene G4 Gene G5 Gene G6 Gene G7 Gene G8 Gene G9 Function sin(x) cos(x) sin(x) ... models for gene regulatory networks Rangel et al [9, 10] apply state-space modeling to T-cell activation data The technique provides a means for constructing reliable gene regulatory networks based ... simple one -to- one regulatory relationships A multiple-input model works for complex many -to- one regulatory relations 2.2 Single-Input Model with Delay In a simple one -to- one regulatory relation,...

Ngày tải lên: 21/06/2014, 20:20

... target genes and call them all “genes.”) These networks are regarded as the “true” regulatory networks for the organisms Gene- expression data is then generated from these “true” regulatory networks; ... identified gene families of interest, we need to build gene trees or assign orthologies for these genes to be able to reconstruct a history of duplications and losses Any error in gene tree reconstruction ... DBNs are used to model regulatory networks, an associated structure-learning algorithm is used to infer the networks from gene- expression data [3,13,14]; so as to avoid overly complex networks, a...

Ngày tải lên: 12/08/2014, 17:20

... according to semantic criteria This allows us to chunk noun phrases generalizing over both POStags and semantic tags Syntacto-semantic chunking was performed to recognize named entities using cascades ... recognize gene noun phrases: [nx gene [dt the] [nnpg CYC1] [gene gene] [in in] [yeast Saccharomyces cerevisiae]] Other syntactic variants, as for example “the glucokinase gene GLK1” are recognized too ... each word (or multiword) of the tokenized corpus Semantic labeling A manually built taxonomy is used to assign semantic labels to tokens The taxonomy consists of gene names, cue words relevant...

Ngày tải lên: 31/03/2014, 03:20

... to such processes, only in principle similar to simple biochemical reactions STOCHASTICITY IN GENETIC REGULATORY NETWORKS There is a large body of theoretical and experimental works devoted to ... solid basis for studying the dynamics of genetic regulatory networks because they recognize the central role of RNAPs in the nonlinear mechanism of gene -to- gene interactions However, it should be ... [26]) There are numerous attempts in the literature to describe the oscillatory behavior of genetic regulatory networks in a linear fashion using the concept of feedback loops and other methods...

Ngày tải lên: 22/06/2014, 22:20

... operate at temperatures near K Due to his novel approach to problem solving, he was awarded the University Analog -to- Digital Conversion Using IF Networks of Florida Tom Scott Memorial Award for Distinction ... The input resistor, RI , was set to a uniform random variable over the range from 666 kΩ to MΩ to discourage neuron synchronization The nonlinearities near 20 kHz are related to the parasitic ... fixed CASCADING NETWORKS By connecting the output of a network of 1-bit A/D converters to the input of another stage, forming a chain, it is possible to cascade multiple networks together In our...

Ngày tải lên: 23/06/2014, 01:20

... approach to learn regulatory codes de-novo from a repository of CRMs A probabilistic graphical model is used to derive the regulatory codes The model is also used to predict novel CRMs Using a ... contain 30,000 to 40,000 genes The gene DNA sequence maps to the protein amino acid sequence through the genetic code In the genetic code each triplet of nucleotides (called „codon‟) maps to a particular ... controlling the transcription of the genes I-1.5 Cis -Regulatory Sequences The DNA sequences where TFs bind in order to regulate gene expression are known as cis -regulatory sequences The DNA region immediately...

Ngày tải lên: 14/09/2015, 14:10

... The term vi is limited to its bounds If the velocity violates this limit, it is set to its proper limit w is the inertia weight factor and in general, it is set according to the following equation: ... pp.813-828 4.1 Real genetic algorithm (RGA) Heuristic methods are able to solve complex optimization problem, and to give a good solution of a certain problem, but they are not assure to reach global ... large constant positive constant M is selected to convert the MLL into a maximum one The coefficient a1 to a3 are optimized by trial and error to 0.237 , 0.315 and 0.448 respectively 3.5 Problem...

Ngày tải lên: 05/09/2013, 15:28

... time, work together to exceed those expectations Students will live up, or down, to your expectations Encourage your students to set high expectations of themselves, then challenge them to exceed ... your administration expects a certain percentage on a test or has a goal to reduce absenteeism, work together with the class to exceed those expectations Whatever expectations your students or their ... our expectations Some expectations will be easy to exceed if students not expect to learn anything, for example Work as a team with your class to exceed expectations If your administration expects...

Ngày tải lên: 06/09/2013, 10:10

... Man, etc) After listening to the entire excerpt, competitors correctly identify the title of the story from a provided list The recorded stories are all classical bedtime stories for young children ... Competitors revealed that they felt less afraid of using their English during game play I also observed that they were more willing to ask questions and think creatively about how to use English to ... translated into most of the major languages worldwide Students should be familiar with those stories This game focuses on gist-listening skills Students only need to catch the key terms to figure...

Ngày tải lên: 06/09/2013, 10:10

... murderer was still at large, I was 26 Having stolen the silver, he looked 27 Soaked to the skin, we reached 28 Sitting/Seated in the front row, and using I saw 29 sitting by the fire, you ... his cage door open and seeing no sign of his keeper, left 34 The government, trying to tax people according to the size of their houses, once put a tax 35 Having heard that the caves were dangerous, ... Becoming tired of my complaints, she turned it off Finding/having found no one at home, he left Hoping to find the will, she searched Having removed all traces of his crime, he left Realizing that he...

Ngày tải lên: 13/09/2013, 21:10

... aren’t able to first reduce the number of ADO.NET-managed rows, you might wish to consider alternatives to LINQ to DataSet LINQ to Entities, discussed in Chapter 19, Using LINQ to Entities,” ... DataTable instances You must link tables together using LINQ’s standard Join operator or use the Where clause to create an implicit join 306 Chapter 18  Using LINQ to DataSet 307 C# // - Explicit ... Writing Queries with LINQ to DataSet With the exception of the new enumerated methods specific to LINQ to DataSet, using ADO.NET DataTable objects in LINQ queries is identical to using standard collection...

Ngày tải lên: 03/10/2013, 00:20