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

We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools....

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Detalles Bibliográficos
Autores principales: Robertson, G., Bilenky, M., Lin, K., He, A., Yuen, W., Dagpinar, M., Varhol, R., Teague, K., Griffith, O. L., Zhang, X., Pan, Y., Hassel, M., Sleumer, M. C., Pan, W., Pleasance, E. D., Chuang, M., Hao, H., Li, Y. Y., Robertson, N., Fjell, C., Li, B., Montgomery, S. B., Astakhova, T., Zhou, J., Sander, J., Siddiqui, A. S., Jones, S. J. M.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347438/
https://www.ncbi.nlm.nih.gov/pubmed/16381958
http://dx.doi.org/10.1093/nar/gkj075
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author Robertson, G.
Bilenky, M.
Lin, K.
He, A.
Yuen, W.
Dagpinar, M.
Varhol, R.
Teague, K.
Griffith, O. L.
Zhang, X.
Pan, Y.
Hassel, M.
Sleumer, M. C.
Pan, W.
Pleasance, E. D.
Chuang, M.
Hao, H.
Li, Y. Y.
Robertson, N.
Fjell, C.
Li, B.
Montgomery, S. B.
Astakhova, T.
Zhou, J.
Sander, J.
Siddiqui, A. S.
Jones, S. J. M.
author_facet Robertson, G.
Bilenky, M.
Lin, K.
He, A.
Yuen, W.
Dagpinar, M.
Varhol, R.
Teague, K.
Griffith, O. L.
Zhang, X.
Pan, Y.
Hassel, M.
Sleumer, M. C.
Pan, W.
Pleasance, E. D.
Chuang, M.
Hao, H.
Li, Y. Y.
Robertson, N.
Fjell, C.
Li, B.
Montgomery, S. B.
Astakhova, T.
Zhou, J.
Sander, J.
Siddiqui, A. S.
Jones, S. J. M.
author_sort Robertson, G.
collection PubMed
description We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.
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spelling pubmed-13474382006-01-25 cisRED: a database system for genome-scale computational discovery of regulatory elements Robertson, G. Bilenky, M. Lin, K. He, A. Yuen, W. Dagpinar, M. Varhol, R. Teague, K. Griffith, O. L. Zhang, X. Pan, Y. Hassel, M. Sleumer, M. C. Pan, W. Pleasance, E. D. Chuang, M. Hao, H. Li, Y. Y. Robertson, N. Fjell, C. Li, B. Montgomery, S. B. Astakhova, T. Zhou, J. Sander, J. Siddiqui, A. S. Jones, S. J. M. Nucleic Acids Res Article We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally. Oxford University Press 2006-01-01 2005-12-28 /pmc/articles/PMC1347438/ /pubmed/16381958 http://dx.doi.org/10.1093/nar/gkj075 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Robertson, G.
Bilenky, M.
Lin, K.
He, A.
Yuen, W.
Dagpinar, M.
Varhol, R.
Teague, K.
Griffith, O. L.
Zhang, X.
Pan, Y.
Hassel, M.
Sleumer, M. C.
Pan, W.
Pleasance, E. D.
Chuang, M.
Hao, H.
Li, Y. Y.
Robertson, N.
Fjell, C.
Li, B.
Montgomery, S. B.
Astakhova, T.
Zhou, J.
Sander, J.
Siddiqui, A. S.
Jones, S. J. M.
cisRED: a database system for genome-scale computational discovery of regulatory elements
title cisRED: a database system for genome-scale computational discovery of regulatory elements
title_full cisRED: a database system for genome-scale computational discovery of regulatory elements
title_fullStr cisRED: a database system for genome-scale computational discovery of regulatory elements
title_full_unstemmed cisRED: a database system for genome-scale computational discovery of regulatory elements
title_short cisRED: a database system for genome-scale computational discovery of regulatory elements
title_sort cisred: a database system for genome-scale computational discovery of regulatory elements
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347438/
https://www.ncbi.nlm.nih.gov/pubmed/16381958
http://dx.doi.org/10.1093/nar/gkj075
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