174 Hits in 4.8 sec

CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining

Carmen Navarro, Francisco J. Lopez, Carlos Cano, Fernando Garcia-Alcalde, Armando Blanco, Leonardo Mariño-Ramírez
2014 PLoS ONE  
CisMiner can be queried for the results presented in this work and can also perform a customized cis-regulatory module prediction on a query set of transcription factor binding sites provided by the user  ...  In this work we present CisMiner, a novel methodology to detect putative CRMs by means of a fuzzy itemset mining approach able to operate at genome-wide scale.  ...  CisMiner is, in this sense, a unique approach for obtaining reliable putative CRMs for whole-genome studies with no prior assumptions about genes or transcription factors involved.  ... 
doi:10.1371/journal.pone.0108065 pmid:25268582 pmcid:PMC4182448 fatcat:gfhsgqb4hbcpdcl2vrx3gj5cwa

Linear fuzzy gene network models obtained from microarray data by exhaustive search

Bahrad A Sokhansanj, J Patrick Fitch, Judy N Quong, Andrew A Quong
2004 BMC Bioinformatics  
We demonstrated our approach with exhaustive search for fuzzy gene interaction models that best fit transcription measurements by microarray of twelve selected genes regulating the yeast cell cycle.  ...  Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome.  ...  Kercher, A. Golumbfskie, B. Pesavento, and K. S. Kim for reviewing drafts of the manuscript and providing important insights. Allan Gu helped with software integration.  ... 
doi:10.1186/1471-2105-5-108 pmid:15304201 pmcid:PMC514698 fatcat:am25xi5ilzbpbc2qkajwnexpfa

The design of transcription-factor binding sites is affected by combinatorial regulation

Yonatan Bilu, Naama Barkai
2005 Genome Biology  
In such a scenario, binding-site fuzziness is a consequence of the presence of multiple binding sites.  ...  Transcription factors regulate gene expression by binding to specific cis-regulatory elements in gene promoters.  ...  A150562 and a grant from the Kahn fund for Systems Biology at the Weizmann institute of science. Y.B. is supported by the Dewey David Stone Postdoctoral Fellowship.  ... 
doi:10.1186/gb-2005-6-12-r103 pmid:16356266 pmcid:PMC1414079 fatcat:dbxh4q2dgbhlthx2pl2ajolkmu

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle

H.-C. Chen, H.-C. Lee, T.-Y. Lin, W.-H. Li, B.-S. Chen
2004 Bioinformatics  
We present a systematic approach to quantitatively characterize the transcriptional regulatory network of the yeast cell cycle.  ...  This approach may be useful for computing the regulatory ability of the transcriptional regulatory networks in more diverse conditions and in more complex eukaryotes. Contact:  ...  ., for grants NSC 91-3112-B-007-002.  ... 
doi:10.1093/bioinformatics/bth178 pmid:15044243 fatcat:ry7yuyvnnbf4vi5kh66nv7ztte

From DNA sequence to transcriptional behaviour: a quantitative approach

Eran Segal, Jonathan Widom
2009 Nature reviews genetics  
| Complex transcriptional behaviours are encoded in the DNA sequences of gene regulatory regions.  ...  An emerging view is that every regulatory sequence is associated with a unique binding affinity landscape for each molecule and, consequently, with a unique set of molecule-binding configurations and transcriptional  ...  Acknowledgements We thank the members of our laboratories for discussions and critical comments on the manuscript.  ... 
doi:10.1038/nrg2591 pmid:19506578 pmcid:PMC2719885 fatcat:pyaaq7m7szg4bifbevn44bjmty

Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae

Tra Thi Vu, Jiri Vohradsky
2006 Nucleic Acids Research  
This study presents a dynamic model of gene expression which allows for identification of transcriptional regulators using time series of gene expression.  ...  Microarray studies are capable of providing data for temporal gene expression patterns of thousands of genes simultaneously, comprising rich but cryptic information about transcriptional control.  ...  Funding to pay the Open Access publication charges for this article was provided by ActinoGEN. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl1001 pmid:17170011 pmcid:PMC1802551 fatcat:fbvnbe7cwve5ngc7yojvnhhhaq

Natural computing methods in bioinformatics: A survey

Francesco Masulli, Sushmita Mitra
2009 Information Fusion  
We utilize the learning ability of neural networks for adapting, uncertainty handling capacity of fuzzy sets and rough sets for modeling ambiguity, and the search potential of genetic algorithms for efficiently  ...  In this article we survey the role of natural computing in the domains of protein structure prediction, microarray data analysis and gene regulatory network generation.  ...  The relationship was represented in terms of rules, linking a transcription factor (TF) to the target gene that it regulates.  ... 
doi:10.1016/j.inffus.2008.12.002 fatcat:hwame6u3svh4jdqb3qfetvzxeq

Recent Computational Approaches to Understand Gene Regulation: Mining Gene Regulation In Silico

I. Abnizova, T. Subhankulova, W. Gilks
2007 Current Genomics  
In eukaryotes, a number of transcription factors often work together in a combinatorial fashion to enable cells to respond to a wide spectrum of environmental and developmental signals.  ...  Cis-regulation of gene expression by the binding of transcription factors is a critical component of cellular physiology.  ...  ACKNOWLEDGEMENTS We are thankful to Graham Ellis for support and to Rene te Boekhorst for hard work with references.  ... 
doi:10.2174/138920207780368150 pmid:18660846 pmcid:PMC2435357 fatcat:ztr3u3c42zazzdp6ug4pwy5l54

Epigenomics and the structure of the living genome

Nir Friedman, Oliver J. Rando
2015 Genome Research  
Work was supported in part by the National Institutes of Health (NIH) grant R01 GM079205 to O.J.R. and N.F., grant R01 HD080224 to O.J.R., European Research Council grant 340712 to N.F., and Israeli Science  ...  Acknowledgments We thank Ronen Sadeh for critical comments on this manuscript.  ...  notably tightly bound transcription factors (TFs) that, in yeast, are known as "general regulatory factors."  ... 
doi:10.1101/gr.190165.115 pmid:26430158 pmcid:PMC4579333 fatcat:j7zeoj7gtvghhjevejbtggr4ke

A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast

Vladimir Filkov, Nameeta Shah
2008 Journal of Computational Biology  
This modularity has a nontrivial, general combinatorial structure that can be studied and generalized to model classes of regulatory systems.  ...  Here, we study computationally the combinatorial nature of transcriptional regulation by assuming a one-to-one relationship between shared patterns in genome-wide gene-expression and cis-region modules  ...  CONCLUSION In this paper, we presented a simple combinatorial model of causal modularity in transcriptional gene regulation.  ... 
doi:10.1089/cmb.2008.0020 pmid:18466069 fatcat:bh4lp34p7bbf7c475crri6r7di

Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks

Chushin Koh, Fang-Xiang Wu, Gopalan Selvaraj, Anthony J. Kusalik
2009 EURASIP Journal on Bioinformatics and Systems Biology  
Based on the state-space approach, we developed a new modeling tool for inferring gene regulatory networks, called time-delayed Gene Regulatory Networks (tdGRNs). tdGRN takes time-delayed regulatory relationships  ...  In addition, a priori biological knowledge from genome-wide location analysis is incorporated into the structure of the gene regulatory network. tdGRN is evaluated on both an artificial dataset and a published  ...  Acknowledgment The authors thank Natural Sciences and Engineering Research Council of Canada (NSERC) for a partial financial support to this research.  ... 
doi:10.1155/2009/484601 pmid:19841683 pmcid:PMC3171427 fatcat:nlnhcx3dwvdpzl2fewyyzknbbq

Genome-Wide Views of Chromatin Structure

Oliver J. Rando, Howard Y. Chang
2009 Annual Review of Biochemistry  
In this review, we discuss the use of genomic technologies to characterize chromatin structure in vivo, with a focus on data from budding yeast and humans.  ...  need to establish faithful gene regulatory mechanisms for cell differentiation. 245  ...  O.J.R. is supported in part by a Career Award in the Biomedical Sciences from the Burroughs Wellcome Fund.  ... 
doi:10.1146/annurev.biochem.78.071107.134639 pmid:19317649 pmcid:PMC2811691 fatcat:ajmebafsgfa3lcao4rt2y45if4

Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

Steven Hahn, Elton T. Young
2011 Genetics  
Many fundamental gene regulatory mechanisms have been conserved in all eukaryotes, and budding yeast has been at the forefront in the discovery and dissection of these conserved mechanisms.  ...  We also examine advances in understanding the RNA polymerase II transcription machinery, conserved coactivator complexes, transcription activation domains, and the cooperation of these factors in gene  ...  However, sequencing of multiple yeast genomes has allowed a bioinformatics approach to largely supplant the classical approach for discovering and characterizing regulatory motifs.  ... 
doi:10.1534/genetics.111.127019 pmid:22084422 pmcid:PMC3213380 fatcat:kik5ysod6bdb5djltodfyx7qqa

Malleable machines take shape in eukaryotic transcriptional regulation

Monika Fuxreiter, Peter Tompa, István Simon, Vladimir N Uversky, Jeffrey C Hansen, Francisco J Asturias
2008 Nature Chemical Biology  
for interactions that convey regulatory information in processes ranging from chromatin remodeling to mRNA processing.  ...  Determining the functional significance of intrinsically disordered protein regions and developing conceptual models of their action will help to illuminate their key role in transcription regulation.  ...  Once the chromatin environment becomes accessible, regulation of the promoter involves the action of regulatory transcription factors, co-activators/co-repressors and the basal transcription machinery.  ... 
doi:10.1038/nchembio.127 pmid:19008886 pmcid:PMC2921704 fatcat:dj6vpbxskfbztaqpo5tvt7la44

Current approaches to gene regulatory network modelling

Thomas Schlitt, Alvis Brazma
2007 BMC Bioinformatics  
We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide  ...  Here we will describe some examples for each of these categories.  ...  Luscombe et al. compiled data from ChIP-on-chip experiments for yeast to construct a network of 142 transcription factors, 3420 target genes and 7074 regulatory interactions [32] .  ... 
doi:10.1186/1471-2105-8-s6-s9 pmid:17903290 pmcid:PMC1995542 fatcat:g7nvzez6cngdnl3ocy7q56z2fa
« Previous Showing results 1 — 15 out of 174 results