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BIOPROSPECTOR: DISCOVERING CONSERVED DNA MOTIFS IN UPSTREAM REGULATORY REGIONS OF CO-EXPRESSED GENES

X. LIU, D. L. BRUTLAG, J. S. LIU
2000 Biocomputing 2001  
BioProspector, a C program using a Gibbs sampling strategy, examines the upstream region of genes in the same gene expression pattern group and looks for regulatory sequence motifs.  ...  The development of genome sequencing and DNA microarray analysis of gene expression gives rise to the demand for data-mining tools.  ...  Lieb, for the valuable RAP1-binding immuno-precipitation and gene expression data. X. Liu is supported by the Lucille P. Markey Biomedical Research Fellowship.  ... 
doi:10.1142/9789814447362_0014 fatcat:6xamdt3rwzay7iwygsduw553eq

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data

Bertrand R Huber, Martha L Bulyk
2006 BMC Bioinformatics  
Applying this motif finding strategy to conserved noncoding regions surrounding co-expressed tissue-specific human genes allowed us to discover both previously known, and many novel candidate, regulatory  ...  A key step in the regulation of gene expression is the sequence-specific binding of transcription factors (TFs) to their DNA recognition sites.  ...  De Masi for beta-testing of software installation.  ... 
doi:10.1186/1471-2105-7-229 pmid:16643658 pmcid:PMC1522027 fatcat:nvkulysidvc5tecxktuxdeb7f4

Analysis of Regulatory Genomics and Gene Expression Pattern of Medicinal Importance Genes of Helicobacter Pylori

Pramod Katara, Ashutosh Singh
2010 Journal of computer science and systems biology  
motif of Oligo and Dyad pattern in studied genes.  ...  motif are the sequence portion which are responsible for gene regulation, by studying them we can control the expression of such genes of interest.  ...  Acknowledgements Authors acknowledge the bioinformatics facility at Department of Bioscience and Biotechnology, Banasthali University, Banasthali for providing essential facilities for completion of this  ... 
doi:10.4172/jcsb.1000049 fatcat:4avh2x7aerc2jbl4y7nco4bhpa

Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes

S. T. Jensen, L. Shen, J. S. Liu
2005 Bioinformatics  
In our approach, de novo discovery methods are used to find motifs conserved by evolution and then a Bayesian hierarchical clustering model is used to cluster these motifs, thereby grouping together genes  ...  Results: We use our framework to predict co-regulated genes in the bacterium Bacillus subtilis using six other closely related bacterial species.  ...  Patrick Eichenberger and Richard Losick for helpful discussions about gene regulation in B.subtilis.  ... 
doi:10.1093/bioinformatics/bti628 pmid:16105899 fatcat:mvhslasu7bglfjsjeebhfplb4i

Identifying target sites for cooperatively binding factors

D. GuhaThakurta, G. D. Stormo
2001 Bioinformatics  
Here we present an algorithm, Co-Bind (for COperative BINDing), for discovering DNA target sites for cooperatively acting transcription factors.  ...  Though developed to model protein-DNA interactions, the scope of Co-Bind may be extended to combinatorial, sequence specific, interactions in other macromolecules.  ...  Chris Workman is thanked for his useful input during development of the method. We thank Chip Lawrence for providing the 1.01.009 version of Gibbs Motif Sampler and instructions on its use.  ... 
doi:10.1093/bioinformatics/17.7.608 pmid:11448879 fatcat:fsjtxfw7k5gttorq6u5qqhoya4

CompMoby: Comparative MobyDick for detection of cis-regulatory motifs

Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch, Hao Li
2008 BMC Bioinformatics  
The CompMoby algorithm was previously shown to identify cis-regulatory binding sites in upstream regions of genes co-regulated in embryonic stem cells.  ...  The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans.  ...  Acknowledgements We would like to thank members of the Li and Ramalho-Santos laboratories for their useful discussion and input on this project.  ... 
doi:10.1186/1471-2105-9-455 pmid:18950538 pmcid:PMC2605473 fatcat:qd4l57l47bbnnnnnwbk23zebme

Page 2349 of Genetics Vol. 172, Issue 4 [page]

2006 Genetics  
Liu, 2001 BioProspector: discover- ing conserved DNA motifs in upstream regulatory regions of co- expressed genes. Pac. Symp. Biocomput., 127-138. MARKSTEIN, M., and M.  ...  Rusrin, 2002 Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1: 1-8. Yusurzal, T. M., and G.  ... 

Comparative Analysis of Regulatory Motif Discovery Tools for Transcription Factor Binding Sites

Wei Wei, Xiao-Dan Yu
2007 Genomics, Proteomics & Bioinformatics  
In the post-genomic era, identif ication of specif ic regulatory motifs or transcription factor binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate transcriptional regulatory  ...  However, these existing methods, based on dif ferent computational algorithms, show diverse motif prediction ef f iciency in non-coding DNA sequences.  ...  Aiguo Li of the National Cancer Institute in NIH for her helpful advice on the manuscript.  ... 
doi:10.1016/s1672-0229(07)60023-0 pmid:17893078 pmcid:PMC5054109 fatcat:xxox63yfmfarzod4in5qe5w2re

Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective

Jun S. Liu, Qing Zhou, X. Shirley Liu, Shane T. Jensen
2004 Statistical Science  
gene regulatory binding motifs.  ...  After reviewing several heuristicsbased computational methods, this article presents a systematic account of Bayesian formulations and solutions to the motif discovery problem.  ...  ACKNOWLEDGMENT Research supported in part by NSF Grant DMS-02-04674 and National Institutes of Health Grant R01 HG02518-01.  ... 
doi:10.1214/088342304000000107 fatcat:4yhj7xqqwzfztkp35sn77j6dsy

Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas

Christophe Liseron-Monfils, Tim Lewis, Daniel Ashlock, Paul D McNicholas, François Fauteux, Martina Strömvik, Manish N Raizada
2013 BMC Plant Biology  
The recent release of the maize genome (Zea mays L.) has facilitated in silico searches for regulatory motifs.  ...  The discovery of genetic networks and cis-acting DNA motifs underlying their regulation is a major objective of transcriptome studies.  ...  for assistance in setting up server access; and Geir Kjetil Sandve and Kjetil Klepper (Norwegian University of Science and Technology, Norway) for assistance with their benchmark data set.  ... 
doi:10.1186/1471-2229-13-42 pmid:23497159 pmcid:PMC3658923 fatcat:2b2czycuyfeqbbvsxv3izxaysq

Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information

Bin Yan, Cinthia Núñez, Toshiyuki Ueki, Abraham Esteve-Núñez, Marko Puljic, Ronald M. Adkins, Barbara A. Methé, Derek R. Lovley, Julia Krushkal
2006 Gene  
The search for conserved overrepresented motifs in co-regulated operons identified likely −35 and −10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were  ...  Gene 384 (2006) 73 -95 www.elsevier.com/locate/gene Abbreviations: COG, clusters of orthologous groups; FDR, the false discovery rate; Hsp20, heat shock protein 20; Lrp, leucine-responsive regulatory protein  ...  Identification of conserved motifs in co-regulated operons In our search for potential regulatory sites affecting expression of co-regulated operons controlled by RpoS, we identified conserved overrepresented  ... 
doi:10.1016/j.gene.2006.06.025 pmid:17014972 fatcat:rlsusy3yi5cqzbq64cnfhpxjcy

Discovering DNA regulatory elements with bacteria

Martha L Bulyk
2005 Nature Biotechnology  
The largest class of these proteins are regulatory transcription factors, which by binding in a sequence-specific fashion to DNA-binding sites in the genome, modulate the expression of their target genes  ...  Using these newly discovered binding site data, they then predicted and experimentally validated two new target genes of Odd.  ...  Although it is currently unclear what is the most appropriate way to measure functional conservation of binding sites, phylogenetic conservation within syntenic regions will likely enrich for regulatory  ... 
doi:10.1038/nbt0805-942 pmid:16082362 pmcid:PMC2720157 fatcat:qp2vxp6vyzdxvewffyx2fwnhci

A survey of motif discovery methods in an integrated framework

Geir Kjetil Sandve, Finn Drabløs
2006 Biology Direct  
There has been a growing interest in computational discovery of regulatory elements, and a multitude of motif discovery methods have been proposed.  ...  This paper presents a survey of methods for motif discovery in DNA, based on a structured and well defined framework that integrates all relevant elements.  ...  Acknowledgements Finn Drabløs was supported by The National Programme for Research in Functional Genomics in Norway (FUGE) in The Research Council of Norway and by The Svanhild and Arne Must Fund for Medical  ... 
doi:10.1186/1745-6150-1-11 pmid:16600018 pmcid:PMC1479319 fatcat:for3d4snx5cljkusk35bmtjq2a

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays

Sonali Mukherjee, Michael F Berger, Ghil Jona, Xun S Wang, Dale Muzzey, Michael Snyder, Richard A Young, Martha L Bulyk
2004 Nature Genetics  
They control the coordinated expression of thousands of genes during normal growth and in response to external stimuli.  ...  In addition to previously identified targets, Abf1, Rap1, and Mig1 bound to 107, 90, and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized  ...  In order to look for evidence for such co-regulatory mechanisms, for each TF we searched the sets of intergenic regions bound only in vitro or only in vivo for secondary DNA sequence motifs.  ... 
doi:10.1038/ng1473 pmid:15543148 pmcid:PMC2692596 fatcat:zyuqqz3dl5ftvn33upxyyk4e3i

Human Upstream and Mouse Upstream: Databases of Promoter Sequences in the Human and Mouse Genomes

Igor Leykin, Ming-Chih J. Kao, Wing Hung Wong
2005 Omics  
Large-scale genome annotations, based largely on gene prediction programs, may be inaccurate in their predictions of transcription start sites, so that the identification of promoter regions remains unreliable  ...  We report the construction of databases of upstream sequences HumanUpstream and MouseUpstream based on information from both the human and mouse genomes and the database of expressed sequence tags (dbEST  ...  BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 127-138. MCGUIRE, A.M., HUGHES, J.D., and CHURCH, G.M. (2000).  ... 
doi:10.1089/omi.2005.9.220 pmid:16209636 fatcat:eackt4dvhngphgx4l5h5qzfp5u
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