title: Finding differentially expressed genes for pattern generation.
abstract: BACKGROUND
  It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation.
  
  
  RESULTS
  We developed two methods which are mainly based on the q-values approach; the first is a direct extension of the q-values approach, while the second uses two approaches: q-values and maximum-likelihood. We present two algorithms for the second method, one for error minimization and the other for confidence bounding. Also, we show how the method called Patterns from Gene Expression (PaGE) (Grant et al., 2000) can benefit from q-values. Finally, we conducted some experiments to demonstrate the effectiveness of the proposed methods; experimental results on a selected dataset (BRCA1 vs BRCA2 tumor types) are provided.
  
  
  BACKGROUND
  alhajj@cpsc.ucalgary.ca.
authors.affiliation: Department of Computer Science, University of Calgary Calgary, Alberta, Canada.
authors.forename: Osman
authors.initials: O
authors.lastname: Abul
authors.forename: Reda
authors.initials: R
authors.lastname: Alhajj
authors.forename: Faruk
authors.initials: F
authors.lastname: Polat
authors.forename: Ken
authors.initials: K
authors.lastname: Barker
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D024682:BRCA2 Protein / Q000235:genetics / Q000378:metabolism*; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism*; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism*; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism*; D016000:Cluster Analysis; D003205:Computing Methodologies; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D044767:Ubiquitin-Protein Ligases
chemical_list: D024682:BRCA2 Protein; D014408:Biomarkers, Tumor; D002352:Carrier Proteins; C111164:BRAP protein, human; D044767:Ubiquitin-Protein Ligases