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cisRED: a database system for genome-scale computational discovery of regulatory elements

G. Robertson
2006 Nucleic Acids Research  
We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (www.cisred. org). The database and high-throughput predictive  ...  ACKNOWLEDGEMENTS We gratefully acknowledge funding from Genome Canada, Genome British Columbia and the BC Cancer Foundation.  ...  In this report, we describe a new cisRED database that contains predictions for whole-genome discovery of regulatory elements in mammals and other eukaryotes.  ... 
doi:10.1093/nar/gkj075 pmid:16698960 pmcid:PMC3303179 fatcat:vfktocbp7nhknov2atxcutukyy

MotifOrganizer a scalable model-based motif clustering tool for mammalian genomes

Zhaohui S Qin
2013 Frontiers in Bioscience (Elite Edition)  
TRANSFAC 4.3. cisRED 5. Discussion 6. Acknowledgement 7. References binding sites using ChIP-Seq data.  ...  In one such study, Robertson et al. described the construction of cisRED, a database that contains predictions from whole-genome discovery of cis-regulatory elements in mammals and other eukaryotes (9  ...  A natural follow-up of large-scale motif discovery efforts like cisRED is to cluster similar motifs in the database into groups.  ... 
doi:10.2741/e659 pmid:23277033 fatcat:yfntc4ykorfxni7nx32edibqge

Post-genomic approaches to exploring neuropeptide gene mis-expression in disease

Alasdair MacKenzie, John P Quinn
2004 Neuropeptides  
In addition, we will describe freely available methods of rapidly and accurately identifying likely neuropeptide gene regulatory regions using computer analysis of newly available mouse, rat, human and  ...  pufferfish (Fugu) genomic sequence.  ...  Acknowledgement We would like to thank Steve Davies for critically reading our manuscript. This work was funded by Tenovus Scotland, the BBSRC, the Wellcome Trust and the MRC.  ... 
doi:10.1016/j.npep.2003.09.004 pmid:15003710 fatcat:dg6uogtlmbcl5lgq7ikpkh3zj4

Large-scale motif discovery using DNA Gray code and equiprobable oligomers

Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh
2011 Computer applications in the biosciences : CABIOS  
Motivation: How to find motifs from genome-scale functional sequences, such as all the promoters in a genome, is a challenging problem.  ...  We also show that the accuracy of our method is superior to that of a leading method, especially for large-scale data and small fractions of motif-containing sequences.  ...  We implement our motif discovery method in C to produce the computer program named 'Hegma' and evaluate the performance of Hegma by using a known database, cisRED (Robertson et al., 2006) .  ... 
doi:10.1093/bioinformatics/btr606 pmid:22057160 pmcid:PMC3244767 fatcat:q2tbz4o345ckpmpvu3fpuacbme

Transcription Factor Map Alignment of Promoter Regions

Enrique Blanco, Xavier Messeguer, Temple F. Smith, Roderic Guigó
2006 PLoS Computational Biology  
Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TFmap alignments are able to uncover conserved regulatory elements, which cannot be detected  ...  We have optimized the parameters of the algorithm in a small, but well-curated, collection of human-mouse orthologous gene pairs.  ...  Acknowledgments The ideas developed in this paper were first explored more than fifteen years ago, when RG was a postdoc with TS.  ... 
doi:10.1371/journal.pcbi.0020049 pmid:16733547 pmcid:PMC1464811 fatcat:5kvbctyg3nbebik2izcqghnwo4

ORegAnno: an open-access community-driven resource for regulatory annotation

O. L. Griffith, S. B. Montgomery, B. Bernier, B. Chu, K. Kasaian, S. Aerts, S. Mahony, M. C. Sleumer, M. Bilenky, M. Haeussler, M. Griffith, S. M. Gallo (+17 others)
2007 Nucleic Acids Research  
ORegAnno is an open-source, open-access database and literature curation system for communitybased annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and  ...  Users can enter or 'check out' papers from the queue for manual curation using a series of user-friendly annotation pages.  ...  We also thank the owners of regulatory sequence databases that made their data available for inclusion in ORegAnno.  ... 
doi:10.1093/nar/gkm967 pmid:18006570 pmcid:PMC2239002 fatcat:a2mf7bj4hrcplodqlcmh62lroe

GW8510 Increases Insulin Expression in Pancreatic Alpha Cells through Activation of p53 Transcriptional Activity

Dina Fomina-Yadlin, Stefan Kubicek, Amedeo Vetere, Kaihui Hu He, Stuart L. Schreiber, Bridget K. Wagner, Kathrin Maedler
2012 PLoS ONE  
A predicted p53 response element in the promoter region of the mouse Ins2 gene was verified by chromatin immunoprecipitation (ChIP).  ...  Conclusions/Significance: The induction of Ins2 by GW8510 occurred through p53 in a JNK-and p38-dependent manner.  ...  Paulk, and A. Shamji for technical assistance and discussion.  ... 
doi:10.1371/journal.pone.0028808 pmid:22242153 pmcid:PMC3252286 fatcat:i5tqaqkyvre37kjlrz53ezz46i

KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis [article]

Obi L. Griffith, Byron J. Gao, Mikhail Bilenky, Yuliya Prichyna, Martin Ester, Steven J.M. Jones
2009 arXiv   pre-print
An OPSM, essentially a pattern-based subspace cluster, is a subset of rows and columns in a data matrix for which all the rows induce the same linear ordering of columns.  ...  Existing OPSM discovery methods do not scale well to increasingly large expression datasets.  ...  they may be regulated by the same transcription factors and regulatory elements.  ... 
arXiv:0904.1931v1 fatcat:6twh54lpfbhlxl3qq4lijclb6a

Poster Presentations

EMBnet Journal
2010 EMBnet journal  
RegulonDB is a database of the regulation of transcription initiation or regulatory network of the cell.  ...  In this sense, RegulonDB is a computational model of mechanisms of transcriptional regulation.  ...  Acknowledgments We acknowledge the support of Dirección General de Servicios de Cómputo Académico, UNAM for the expansion of the national node, as well as to Jérôme Verleyen and Roberto Rodriguez from  ... 
doi:10.14806/ej.16.a.154 fatcat:gijtt5n3njhzfbfvp7zc7qaitq

Genomic Features of the Human Dopamine Transporter Gene and Its Potential Epigenetic States: Implications for Phenotypic Diversity

Elena Shumay, Joanna S. Fowler, Nora D. Volkow, Axel Imhof
2010 PLoS ONE  
We propose that this unique combination of the genomic features and the regulatory attributes enables the differential expression of the DAT1 gene and fulfills seemingly contradictory demands to its regulation  ...  region-specific DAT expression, so enabling multiple regulatory modes.  ...  Ruben Baler for helpful discussions and suggestions on the organization of the manuscript, Dr. Fritz Henn for long-standing support, and Dr. Avril Woodhead for editing.  ... 
doi:10.1371/journal.pone.0011067 pmid:20548783 pmcid:PMC2883569 fatcat:ne7rn76wtnedfjvjvld73dda5i

EMBnet.journal 16 Suppl. A

EMBnet Journal
2010 EMBnet journal  
Dear reader, This issue reflects a radical move of EMBnet. The 20-year anniversary for EMBnet was celebrated the year 2008 at Martina Franca, Italy.  ...  EMBnet has grown out of its original shape as a European network into a true global organization encompassing all continents.  ...  the support of Dirección General de Servicios de Cómputo Académico, UNAM for the expansion of the national node, as well as to Jérôme Verleyen and Roberto Rodriguez from the Institute of Biotechnology  ... 
doi:10.14806/ej.16.a.156 fatcat:m3hkdlxdfzdovfgg7ke3xwygn4

From genes to functional classes in the study of biological systems

Fátima Al-Shahrour, Leonardo Arbiza, Hernán Dopazo, Jaime Huerta-Cepas, Pablo Mínguez, David Montaner, Joaquín Dopazo
2007 BMC Bioinformatics  
motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies.  ...  Conclusion: Methods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale  ...  The Functional Genomics node (INB) is supported by Fundación Genoma España.  ... 
doi:10.1186/1471-2105-8-114 pmid:17407596 pmcid:PMC1853114 fatcat:l4qti6dx7va6ppgco7f6ejih4y

Beyond the Gene List: Exploring Transcriptomics Data in Search for Gene Function, Trait Mechanisms and Genetic Architecture [chapter]

Bregje Wertheim
2012 Functional Genomics  
BW was supported by funding from the Netherlands Organization for Scientific Research (NWO) (Vidi grant no. 864.08.008).  ...  Acknowledgement I thank Eric Blanc and Eugene Schuster for their advice and our valuable discussions on the various bioinformatics approaches in gene expression studies.  ...  Using the cisRED database [25] as a first exploration of these novel motifs, two of these motifs were retrieved as a predicted regulatory element in the human genome sequences, including a hit in the  ... 
doi:10.5772/48239 fatcat:ulcvfcwl2fg2znaq7fxwl2gvbi

Comprehensive Analysis of the Palindromic Motif TCTCGCGAGA: A Regulatory Element of the HNRNPK Promoter

M. Mikula, P. Gaj, K. Dzwonek, T. Rubel, J. Karczmarski, A. Paziewska, A. Dzwonek, P. Bragoszewski, M. Dadlez, J. Ostrowski
2010 DNA Research  
We discovered that out of the four potential HNRNPK promoters tested, the one containing the palindromic motif TCTCGCGAGA exhibited the highest activity in a reporter system assay.  ...  Definitive identification of promoters, their cis-regulatory motifs, and their trans-acting proteins requires experimental analysis.  ...  Acknowledgements: We thank Lucjan Wyrwicz for computational identification of potential HNRNPK promoters.  ... 
doi:10.1093/dnares/dsq016 pmid:20587588 pmcid:PMC2920758 fatcat:7jliducthzdwpj5vazu32ssuea

De novo detection of regulatory elements in the nematode Caenorhabditis elegans

Monica Celia Sleumer
2009
The availability of high-throughput gene expression data and completely sequenced genomes from eight species of nematodes has provided an opportunity to identify novel cis-regulatory elements in the promoter  ...  This is the first catalogue of annotated conserved upstream elements for nematodes and can be used to find putative regulatory elements, improve gene models, discover novel RNA genes, and understand the  ...  Proc Natl Acad Sci U S A 102: 1560-1565. 81. Robertson G, Bilenky M, Lin K, He A, Yuen W et al. (2006) cisRED: a database system for genome-scale computational discovery of regulatory elements.  ... 
doi:10.14288/1.0067459 fatcat:r4l3pw5aavhpvb6znnpkff3f2q
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