Phase-independent rhythmic analysis of genome-wide expression patterns.
We introduce a model-based analysis technique for extracting and characterizing rhythmic expression profiles from genome-wide DNA microarray hybridization data. These patterns are clues to discovering rhythmic genes implicated in cell-cycle, circadian, or other biological processes. The algorithm, implemented in a program called RAGE (Rhythmic Analysis of Gene Expression), decouples the problems of estimating a pattern's wavelength and phase. Our algorithm is linear-time in frequency and phase resolution, an improvement over previous quadratic-time approaches. Unlike previous approaches, RAGE uses a true distance metric for measuring expression profile similarity, based on the Hausdorff distance. This results in better clustering of expression profiles for rhythmic analysis. The confidence of each frequency estimate is computed using Z-scores. We demonstrate that RAGE is superior to other techniques on synthetic and actual DNA microarray hybridization data. We also show how to replace the discretized phase search in our method with an exact (combinatorially precise) phase search, resulting in a faster algorithm with no complexity dependence on phase resolution.
Langmead
Christopher James
CJ
Dartmouth Computer Science Department, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA.
Yan
Anthony K
AK
McClung
C Robertson
CR
Donald
Bruce Randall
BR
D000465:Algorithms; D000818:Animals; D017489:CDC28 Protein Kinase, S cerevisiae / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D002940:Circadian Rhythm / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D004330:Drosophila / Q000235:genetics; D019204:GTP-Binding Proteins / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data
C082279:CDC15 protein; D018797:Cell Cycle Proteins; D017489:CDC28 Protein Kinase, S cerevisiae; D019204:GTP-Binding Proteins