title: Thermodynamic scaling behavior in genechips.
abstract: BACKGROUND
  Affymetrix Genechips are characterized by probe pairs, a perfect match (PM) and a mismatch (MM) probe differing by a single nucleotide. Most of the data preprocessing algorithms neglect MM signals, as it was shown that MMs cannot be used as estimators of the non-specific hybridization as originally proposed by Affymetrix. The aim of this paper is to study in detail on a large number of experiments the behavior of the average PM/MM ratio. This is taken as an indicator of the quality of the hybridization and, when compared between different chip series, of the quality of the chip design.
  
  
  RESULTS
  About 250 different GeneChip hybridizations performed at the VIB Microarray Facility for Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana were analyzed. The investigation of such a large set of data from the same source minimizes systematic experimental variations that may arise from differences in protocols or from different laboratories. The PM/MM ratios are derived theoretically from thermodynamic laws and a link is made with the sequence of PM and MM probe, more specifically with their central nucleotide triplets.
  
  
  CONCLUSIONS
  The PM/MM ratios subdivided according to the different central nucleotides triplets follow qualitatively those deduced from the hybridization free energies in solution. It is shown also that the PM and MM histograms are related by a simple scale transformation, in agreement with what is to be expected from hybridization thermodynamics. Different quantitative behavior is observed on the different chip organisms analyzed, suggesting that some organism chips have superior probe design compared to others.
authors.affiliation: Institute for Theoretical Physics, Katholieke Universiteit Leuven, Celestijnenlaan 200D, B-3000 Leuven, Belgium. alessandro.ferrantini@fys.kuleuven.be
authors.forename: Alessandro
authors.initials: A
authors.lastname: Ferrantini
authors.forename: Joke
authors.initials: J
authors.lastname: Allemeersch
authors.forename: Paul
authors.initials: P
authors.lastname: Van Hummelen
authors.forename: Enrico
authors.initials: E
authors.lastname: Carlon
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000378:metabolism; D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D008956:Models, Chemical; D009693:Nucleic Acid Hybridization; D009711:Nucleotides / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D009711:Nucleotides; D012313:RNA; D004247:DNA