Bioinformatics, Vol 14, 48-54, Copyright © 1998 by Oxford University Press
TL Bailey and M Gribskov
MOTIVATION: To illustrate an intuitive and statistically valid method for
combining independent sources of evidence that yields a p-value for the
complete evidence, and to apply it to the problem of detecting simultaneous
matches to multiple patterns in sequence homology searches. RESULTS: In
sequence analysis, two or more (approximately) independent measures of the
membership of a sequence (or sequence region) in some class are often
available. We would like to estimate the likelihood of the sequence being a
member of the class in view of all the available evidence. An example is
estimating the significance of the observed match of a macromolecular
sequence (DNA or protein) to a set of patterns (motifs) that characterize a
biological sequence family. An intuitive way to do this is to express each
piece of evidence as a p-value, and then use the product of these p-values
as the measure of membership in the family. We derive a formula and
algorithm (QFAST) for calculating the statistical distribution of the
product of n independent p-values. We demonstrate that sorting sequences by
this p-value effectively combines the information present in multiple
motifs, leading to highly accurate and sensitive sequence homology
searches.
ARTICLES
Combining evidence using p-values: application to sequence homology searches
San Diego Supercomputer Center, CA 92186-9784, USA.
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S. Crosson, P. T. McGrath, C. Stephens, H. H. McAdams, and L. Shapiro Conserved modular design of an oxygen sensory/signaling network with species-specific output PNAS, May 31, 2005; 102(22): 8018 - 8023. [Abstract] [Full Text] [PDF]
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W. R. Atchley and A. D. Fernandes Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network PNAS, May 3, 2005; 102(18): 6401 - 6406. [Abstract] [Full Text] [PDF]
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A. Rodrigue, G. Effantin, and M.-A. Mandrand-Berthelot Identification of rcnA (yohM), a Nickel and Cobalt Resistance Gene in Escherichia coli J. Bacteriol., April 15, 2005; 187(8): 2912 - 2916. [Abstract] [Full Text] [PDF]
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K. A. Salmon, S.-p. Hung, N. R. Steffen, R. Krupp, P. Baldi, G. W. Hatfield, and R. P. Gunsalus Global Gene Expression Profiling in Escherichia coli K12: EFFECTS OF OXYGEN AVAILABILITY AND ArcA J. Biol. Chem., April 15, 2005; 280(15): 15084 - 15096. [Abstract] [Full Text] [PDF]
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V. Atalay and R. Cetin-Atalay Implicit motif distribution based hybrid computational kernel for sequence classification Bioinformatics, April 15, 2005; 21(8): 1429 - 1436. [Abstract] [Full Text] [PDF]
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S. Hamimes, H. Arakawa, A. Z. Stasiak, A. M. Kierzek, S. Hirano, Y.-G. Yang, M. Takata, A. Stasiak, J.-M. Buerstedde, and E. Van Dyck RDM1, a Novel RNA Recognition Motif (RRM)-containing Protein Involved in the Cell Response to Cisplatin in Vertebrates J. Biol. Chem., March 11, 2005; 280(10): 9225 - 9235. [Abstract] [Full Text] [PDF]
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H. Weber, T. Polen, J. Heuveling, V. F. Wendisch, and R. Hengge Genome-Wide Analysis of the General Stress Response Network in Escherichia coli: {sigma}S-Dependent Genes, Promoters, and Sigma Factor Selectivity J. Bacteriol., March 1, 2005; 187(5): 1591 - 1603. [Abstract] [Full Text] [PDF]
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Y. Barash, G. Elidan, T. Kaplan, and N. Friedman CIS: compound importance sampling method for protein-DNA binding site p-value estimation Bioinformatics, March 1, 2005; 21(5): 596 - 600. [Abstract] [Full Text] [PDF]
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C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, F. Tekaia, O. Bader, A. Albrecht, L. Castillo, A. Dominguez, et al. CandidaDB: a genome database for Candida albicans pathogenomics Nucleic Acids Res., January 1, 2005; 33(suppl_1): D353 - D357. [Abstract] [Full Text] [PDF]
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D. J. Galgoczy, A. Cassidy-Stone, M. Llinas, S. M. O'Rourke, I. Herskowitz, J. L. DeRisi, and A. D. Johnson Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae PNAS, December 28, 2004; 101(52): 18069 - 18074. [Abstract] [Full Text] [PDF]
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