Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules-Reference-Cited by-同舟云学术

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Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

Published:2007-10-10 Issue:1 Volume:2 Page:
ISSN:1748-7188
Container-title:Algorithms for Molecular Biology
language:en
Short-container-title:Algorithms Mol Biol

Author:

Boeva Valentina,Clément Julien,Régnier Mireille,Roytberg Mikhail A,Makeev Vsevolod J

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computational Theory and Mathematics,Molecular Biology,Structural Biology

Link

http://link.springer.com/content/pdf/10.1186/1748-7188-2-13.pdf

Reference67 articles.

1. MacIsaac KD, Fraenkel E: Practical strategies for discovering regulatory DNA sequence motifs. PloS Comput Biol. 2006, 2 (4): e36- 10.1371/journal.pcbi.0020036

2. Sandve GK, Drablos F: A survey of motif discovery methods in an integrated framework. Biol Direct. 2006, 1: 11- 10.1186/1745-6150-1-11

3. Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, van de Peer Y: Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 2003, 132 (3): 1162-1176. Review. 10.1104/pp.102.017715

4. Bulyk ML: DNA microarray technologies for measuring protein-DNA interactions. Curr Opin Biotechnol. 2006, 17 (4): 422-30. 10.1016/j.copbio.2006.06.015

5. Harbison CT, Gordon B, Lee TI, Rinaldi NJ, Macisaac KD, Danford T, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature. 2004, 431: 99-104. 10.1038/nature02800

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1. Aho-Corasick automaton minimization. Application to the computation of pattern occurrences P-value;Proceedings of the International Conference "Mathematical Biology and Bioinformatics";2022-10-27

2. Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments;Algorithms for Molecular Biology;2018-12

3. An efficient method for significant motifs discovery from multiple DNA sequences;Journal of Bioinformatics and Computational Biology;2017-08

4. Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells;Frontiers in Genetics;2016-02-23

5. Characterization of the doublesex gene within the Culex pipiens complex suggests regulatory plasticity at the base of the mosquito sex determination cascade;BMC Evolutionary Biology;2015-06-11

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