Inference of transcriptional regulation relationships from gene expression data.
BACKGROUND
In order to find gene regulatory networks from microarray data, it is important to first find direct regulatory relationships between pairs of genes.


RESULTS
We propose a new method for finding potential regulatory relationships between pairs of genes from microarray time series data and apply it to expression data for cell-cycle related genes in yeast. We compare our algorithm, dubbed the event method, with the earlier correlation method and the edge detection method by Filkov et al. When tested on known transcriptional regulation genes, all three methods are able to find similar numbers of true positives. The results indicate that our algorithm is able to identify true positive pairs that are different from those found by the two other methods. We also compare the correlation and the event methods using synthetic data and find that typically, the event method obtains better results. AVALIABILITY: software is available upon request.
Kwon
Andrew T
AT
Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.
Hoos
Holger H
HH
Ng
Raymond
R
D000465:Algorithms; D020137:Base Pair Mismatch / Q000235:genetics; D017489:CDC28 Protein Kinase, S cerevisiae / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D003198:Computer Simulation; D030561:Databases, Nucleic Acid; D005656:Fungal Proteins / Q000235:genetics; D019204:GTP-Binding Proteins / Q000235:genetics; D005786:Gene Expression Regulation / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D014158:Transcription, Genetic / Q000235:genetics*
C082279:CDC15 protein; D018797:Cell Cycle Proteins; D005656:Fungal Proteins; D017489:CDC28 Protein Kinase, S cerevisiae; D019204:GTP-Binding Proteins