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Topic: Gene regulatory network

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	Gene regulatory network - Wikipedia, the free encyclopedia
		A gene regulatory network (also called a GRN or genetic regulatory network) is a collection of DNA segments in a cell which interact with each other and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.
		Genes can be viewed as nodes in a complex network, with input being proteins such as transcription factors, and outputs being the level of gene expression.
		For a gene, "on" corresponds to the gene being expressed; for inputs and outputs, "on" corresponds to the substance being present.
	en.wikipedia.org /wiki/Gene_regulatory_network (552 words)

	Gene Networks (Site not responding. Last check: 2007-11-06)
		A gene regulatory network (also called a GRN or genetic regulatory network,) is a collection of DNA segments in a cell which interact with each other and with other substances in the cell, thereby governing the rates at which genes are transcribed into mRNA.
		Genes can be viewed as nodes in such a network, with input being proteins such as transcription factors, and outputs being the level of gene expression.
		The gene networks are only beginning to be understood, and it is a next step for biology to attempt to deduce the functions for each gene "node", to assist in modeling behaviour of a cell.
	cnx.org /content/m12383/latest (784 words)

	Gene Regulatory Networks
		Gene regulatory networks (GRNs) are the on-off switches and rheostats of a cell operating at the gene level.
		Beyond GRN boundaries are signaling responses and feedbacks, such as those that drive bacterial chemotaxis, which do not involve regulation of gene expression but instead act directly on proteins and protein machine assemblies (dashed arrows).
		This was shown by microarray gene chip analyses in yeast cells, and each gene was found to possess a similar cis-regulatory DNA sequence that mediates binding of a particular transcription factor.
	doegenomestolife.org /science/generegulatorynetwork.shtml (1067 words)

	Gene regulatory network: Encyclopedia topic (Site not responding. Last check: 2007-11-06)
		Genes can be viewed as nodes in a network (network: (electronics) a system of interconnected electronic components or circuits), with input being proteins such as transcription factor (transcription factor: in molecular biology, a transcription factor is a protein that binds dna at a...
		The gene networks are only beginning to be understood, and it is a next step for biology to attempt to deduce the functions for each gene "node", to assist in modeling behaviour of a cell (see systems biology (systems biology: systems biology is an academic field that seeks to integrate high-throughput biological studies...
		Each gene, each input, and each output is represented by a node in a directed graph (directed graph: more facts about this subject) in which there is an arrow from one node to another if and only if there is a causal link between the two nodes.
	www.absoluteastronomy.com /reference/gene_regulatory_network (728 words)

	Regulatory sequence - Wikipedia, the free encyclopedia
		A regulatory sequence (also called regulatory region or ~ element) is a promoter, enhancer or other segment of DNA where regulatory proteins such as transcription factors bind preferentially.
		They control gene expression and thus protein expression.
		Regulatory sequences can also be found on messenger RNA, but they are generally not as well studied as those in DNA.
	en.wikipedia.org /wiki/Regulatory_sequence (93 words)

	Caltech Authors - Developmental gene regulatory network architecture across 500 million years of echinoderm evolution
		A relevant set of regulatory genes was isolated from the starfish Asterina miniata, their expression patterns determined, and effects on the other genes of perturbing the expression of each were demonstrated.
		A three-gene feedback loop that is a fundamental feature of the sea urchin GRN for endoderm specification is found in almost identical form in the starfish: a detailed element of GRN architecture has been retained since the Cambrian Period in both echinoderm lineages.
		A regulatory gene used to drive skeletogenesis in the sea urchin is used entirely differently in the starfish, where it responds to endomesodermal inputs that do not affect it in the sea urchin embryo.
	resolver.caltech.edu /CaltechAUTHORS:HINpnas03 (443 words)

	Transcriptional Regulatory Network
		How a collection of regulatory proteins associates with genes across a genome can be described as a transcriptional regulatory network.
		Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this map of the transcriptional regulatory network describes potential pathways yeast cells can use to regulate global gene expression programs.
		The network map reveals that gene expression programs and cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators.
	web.wi.mit.edu /young/regulator_network (163 words)

	Endomesoderm Model
		BioTapestry organizes the network model into four levels that are outlined in a tree view on the left side of the window.
		The architecture of the network is based on perturbation and expression data, on data from cis-regulatory analyses for several genes, and on other experiments discussed in text.
		Many genes are initially expressed over broader ranges, and their expression later resolves to the definitive domains indicated by their backgrounds.
	sugp.caltech.edu /endomes (2061 words)

	de la Fuente, et al. 2001
		Gene regulatory interactions are quantified through "regulatory strengths" which are determined from co-responses of messenger RNA to a common perturbation.
		In cases where one cannot measure the expression of all the genes or when it is not convenient or when their transcription rate is not easily perturbed), the method has to be applied only to a subset of the genes.
		For example it may be that the products of gene A and gene B have to bind before being able to activate gene C. Because these may be frequent, it is relevant to see how our method performs with such networks.
	staff.vbi.vt.edu /mendes/icsb01/supplement.html (2053 words)

	IUA-Seminar: Large scale modeling of gene regulatory networks
		The perhaps most important signaling network in living cells is constituted by the interactions of proteins with the genome -- the gene regulatory network of the cell.
		After a brief description of the biological principles of gene regulation and the novel data basis provided by genome wide expression measurements by DNA microarrays, I will summarize a set of recent data driven approaches for modeling gene regulatory networks based on gene expression data.
		The gene expression profiles from the different patients is put in a 2D array where each column is one of the profiles, and that array is 2D-hierarchical clustered.
	www.iua.upf.es /activitats/semirec/MartinStetter (1169 words)

	CiteULike: Gene regulatory network growth by duplication. (Site not responding. Last check: 2007-11-06)
		We are beginning to elucidate transcriptional regulatory networks on a large scale and to understand some of the structural principles of these networks, but the evolutionary mechanisms that form these networks are still mostly unknown.
		The transcriptional interactions in regulatory networks consist of multiple components, and duplication processes that generate new interactions would need to be more complex.
		Gene duplication has had a key role in network evolution: more than one-third of known regulatory interactions were inherited from the ancestral transcription factor or target gene after duplication, and roughly one-half of the interactions were gained during divergence after duplication.
	www.citeulike.org /user/balicea/article/2124 (256 words)

	Citebase - Self-organization of gene regulatory network motifs enriched with short transcript's half-life transcription ...
		Self-organization of gene regulatory network motifs enriched with short transcript's half-life transcription factors
		Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks.
		The large ratio of genes to transcription factors (TFs) in genomes leads to a sharing of TFs by motifs and is sufficient to result in network self-organization.
	citebase.eprints.org /cgi-bin/citations?id=oai:arXiv.org:q-bio/0504025 (306 words)

	A smooth response surface algorithm for constructing gene regulatory network
		A smooth response surface algorithm is developed as an elaborate data mining technique for analyzing gene expression data and constructing gene regulatory network.
		A diagnostic strategy is built into the algorithm to evaluate the scores of the triplets so that those with low scores are kept and a regulatory network is constructed based on this information and existing biological knowledge.
		Hongquan Xu, Peiru Wu, CFJ Wu, Carl Tidwell, and Yixin Wang, "A smooth response surface algorithm for constructing gene regulatory network" (January 1, 2001).
	repositories.cdlib.org /uclastat/papers/2001010106 (240 words)

	Research in Gene Regulatory Networks (Site not responding. Last check: 2007-11-06)
		Several ORNL and collaborative projects are developing computational and experimental methods to identify Gene Regulatory Networks (GRNs), the integrations of genes, regulatory DNA elements, and transcription factor proteins that control the activity of cellular and biochemical pathways.
		Gene expression and levels of the resulting protein products are tightly controlled by complex interactions between transcriptional regulation, translational control, and mRNA and protein stability.
		Gene networks are thus important in transducing genetic signals into phenotypic variation and integrating genomic information, environmental cues, and physiological or developmental stimuli.
	genereg.ornl.gov (407 words)

	Gene Cluster Regulatory Network to Drug Target Identification by using transcriptional profile of Plasmodium falciparum (Site not responding. Last check: 2007-11-06)
		In this study, Plasmodium falciparum, a strain that causes malaria, was studied to infer its possible gene cluster regulatory network from transcription data.
		With the hypothesis that genes in the same cluster may be regulated by the same set of transcription factors (TFs), the upstream sequences of those genes in each cluster were analyzed by using an upstream sequence analysis tool to determine common regulatory motifs.
		At the end, a regulatory network of P. falciparum that interconnects gene clusters to TFs to gene clusters was constructed.
	www.iscb.org /ismb2004/posters/saowalak.kalATbiotec.or.th_171.html (408 words)

	A Gene Regulatory Network for Cell Differentiation in Caenorhabditis elegans (ResearchIndex)
		A Gene Regulatory Network for Cell Differentiation in Caenorhabditis elegans
		6 A gene network approach to modeling early neurogenesis in Dr..
		1 Structure and dyanmics of a gene network model with RNA regu..
	citeseer.ist.psu.edu /651532.html (620 words)

	A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is ...
		Network nodes represent active proteins of corresponding genes, and the edges represent the regulatory interactions between node pairs (arrows are positive, and blunt-end lines are negative).
		for the pair-rule genes in Drosophila (Albert and Othmer, 2003
		Albert, R., and Othmer, H.G. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster.
	www.plantcell.org /cgi/content/full/16/11/2923 (8174 words)

	A smooth response surface algorithm for constructing a gene regulatory network -- Xu et al. 11 (1): 11 -- Physiological ...
		A smooth response surface algorithm for constructing a gene regulatory network -- Xu et al.
		For each triplet of genes, a lack-of-fit formula is used to filter the triplets from the initial screening.
		A predicted gene regulatory network for the microarray data.
	physiolgenomics.physiology.org /cgi/content/full/11/1/11 (4452 words)

	Evolution of transcription factors and the gene regulatory network in Escherichia coli -- Madan Babu and Teichmann 31 ...
		The direct number of genes regulated is represented on the x axis and the indirect number of genes on the y axis.
		The global regulators, which are marked on the graph regulate a large number of genes, and participate in regulatory cascades, resulting in indirect regulation of genes.
		In the first example, three genes forming part of the same operon are homologous to three genes in separate operons, all regulated by fur.
	nar.oxfordjournals.org /cgi/content/full/31/4/1234 (4939 words)

	Developmental gene regulatory network architecture across 500 million years of echinoderm evolution -- Hinman et al. ...
		The genes krox, otx, bra, foxa, and gatae are all expressed within the endomesoderm and are required for its correct specification.
		purpuratus, the tbr gene, its downstream target genes, and its upstream regulators are all expressed in the micromere/skeletogenic lineage and are necessary for its normal specification.
		The positive regulatory feedback loops among krox, otx, and gatae that are present in both taxa are bold.
	www.pnas.org /cgi/content/full/100/23/13356 (4313 words)

	Gene-O-Matic: Regulatory Network Simulation in Multicellular Organisms (Site not responding. Last check: 2007-11-06)
		These events can be controlled by the regulatory network, or by a database of recorded cell positions.
		In addition, the cells have a state composed of the presence and activity of all relevant regulatory molecules.
		By modifying the regulatory network, the phenotype of mutants can also be reproduced accurately.
	www.iscb.org /ismb2003/posters/u.platzerATdkfz.de_59.html (346 words)

	Publications
		Davidson, E.H., McClay, D.R. and Hood, L. (2003) Regulatory gene networks and the properties of the developmental process.
		Hinman, V.F. and Davidson, E.H. Expression of a gene encoding a Gata transcription factor during embryogenesis of the starfish Asterina miniata.
		Hinman, V.F., Nguyen, A., Cameron, R.A. and Davidson, E.H. Developmental gene regulatory network architecture across 500 MYA of echinoderm evolution.
	www.its.caltech.edu /~mirsky/pubs.htm (592 words)

	A Smooth Response Surface Algorithm for Constructing Gene Regulatory Network (ResearchIndex) (Site not responding. Last check: 2007-11-06)
		Abstract: A smooth response sur face algorithm is developed as an elaborate data mining technique for analyzing gene expression data and constructing gene regulatory network.
		A threedimensional smooth response surface is generated to capture the biological relationship between the target and activator-repressor.
		2 Regulation of the yeast CYT1 gene encoding cytochrome c 1 by..
	citeseer.ist.psu.edu /476961.html (468 words)

	Developmental gene regulatory network architecture across 500 million years of echinoderm evolution -- Hinman et al., ...
		Developmental gene regulatory network architecture across 500 million years of echinoderm evolution -- Hinman et al., 10.1073/pnas.2235868100 -- Proceedings of the National Academy of Sciences
		To whom correspondence should be addressed at: Division of Biology 156-29, Pasadena, CA 91125.
		Gene Regulatory Networks and the Evolution of Animal Body Plans
	www.pnas.org /cgi/content/abstract/2235868100v1 (433 words)

	GENE REGULATORY NETWORK IDENTIFICATION AND VISUALIZATION (Site not responding. Last check: 2007-11-06)
		This program aims to reconstruct the cellular processes, metabolic potential (metabolome) and gene regulatory networks of selected gram-positive Bacteria and Archaea, by in silico analysis of all proteins encoded by their chromosome.
		This should lead to important advances in the understanding of prokaryote evolution, and will contribute to the prediction of their metabolic functions.
		development of dynamical system modelling and simulation for gene regulatory network identification, combined with interactive tools for network visualization.
	www.cs.rug.nl /~roe/BMI/BMI.html (208 words)

	Citebase - Robustness, Stability and Efficiency of Phage lambda Gene Regulatory Network: Dynamical Structure Analysis
		Robustness, Stability and Efficiency of Phage lambda Gene Regulatory Network: Dynamical Structure Analysis
		Authors: Zhu, X. Yin, L. Hood, L. Ao, P. Based on our physical and biological studies we have recently developed a mathematical framework for the analysis of nonlnear dynamics.
		The dynamical structure analysis is illustrated in detail by the study of stability, robustness, and efficiency of the simplest gene regulatory network of phage lambda.
	citebase.eprints.org /cgi-bin/citations?id=oai:arXiv.org:q-bio/0403016 (220 words)

	Accelerating Gene Regulatory Network Modeling Using Grid-Based Simulation -- McCollum et al. 80 (45): 231 -- SIMULATION
		Accelerating Gene Regulatory Network Modeling Using Grid-Based Simulation -- McCollum et al.
		Modeling gene regulatory networks has, in some cases, enabled
		is limited by the computational complexity of gene regulatory
	sim.sagepub.com /cgi/content/abstract/80/4-5/231 (157 words)

	A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is ...
		A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profiles -- Espinosa-Soto et al., 10.1105/tpc.104.021725 -- THE PLANT CELL
		that the cell types recovered depend on the network architecture
		rather than on specific values of the model's gene interaction
	www.plantcell.org /cgi/content/short/tpc.104.021725v1 (482 words)

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