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BIOPROSPECTOR: DISCOVERING CONSERVED DNA MOTIFS IN UPSTREAM REGULATORY REGIONS OF CO-EXPRESSED GENES
2000
Biocomputing 2001
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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
2006
BMC Bioinformatics
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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
2010
Journal of computer science and systems biology
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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
2005
Bioinformatics
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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
2001
Bioinformatics
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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
2008
BMC Bioinformatics
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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
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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
2007
Genomics, Proteomics & Bioinformatics
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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
2004
Statistical Science
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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
2013
BMC Plant Biology
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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
2006
Gene
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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
2005
Nature Biotechnology
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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
2006
Biology Direct
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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
2004
Nature Genetics
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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
2005
Omics
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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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