title: Statistical analysis of a small set of time-ordered gene expression data using linear splines.
abstract: BACKGROUND
  Recently, the temporal response of genes to changes in their environment has been investigated using cDNA microarray technology by measuring the gene expression levels at a small number of time points. Conventional techniques for time series analysis are not suitable for such a short series of time-ordered data. The analysis of gene expression data has therefore usually been limited to a fold-change analysis, instead of a systematic statistical approach.
  
  
  METHODS
  We use the maximum likelihood method together with Akaike's Information Criterion to fit linear splines to a small set of time-ordered gene expression data in order to infer statistically meaningful information from the measurements. The significance of measured gene expression data is assessed using Student's t-test.
  
  
  RESULTS
  Previous gene expression measurements of the cyanobacterium Synechocystis sp. PCC6803 were reanalyzed using linear splines. The temporal response was identified of many genes that had been missed by a fold-change analysis. Based on our statistical analysis, we found that about four gene expression measurements or more are needed at each time point.
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. mdehoon@ims.u-tokyo.ac.jp
authors.forename: M J L
authors.initials: MJ
authors.lastname: De Hoon
authors.forename: S
authors.initials: S
authors.lastname: Imoto
authors.forename: S
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D000458:Cyanobacteria / Q000145:classification / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics*; D016013:Likelihood Functions; D016014:Linear Models; D008957:Models, Genetic; D015233:Models, Statistical; D015203:Reproducibility of Results; D018401:Sample Size; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity; D013269:Stochastic Processes; D013997:Time Factors
chemical_list: D004269:DNA, Bacterial