title: Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks.
abstract: Through computational analysis of high-performance liquid chromatography (HPLC) traces we find correlations between secondary metabolites and growth conditions of six varieties of barley. Using artificial neural networks, it was possible to classify chromatograms for which the varieties were fertilized by nitrogen and treated by fungicide. For each variety of barley we could also differentiate it from the others. Surprisingly, all these classification tasks could be solved successfully by a simple network with no hidden units. When adding to the methodology pruning of the network weights, we were able to reduce the set of peaks in the chromatograms and obtain a necessary subset from which the growth conditions and differentiation may be decided. In some instances, more complex networks with hidden units could lead to a further reduction of the number of peaks used. In most cases, far more than half of the peaks are redundant. We find that it requires fewer information-rich peaks to perform the variety differentiation tasks than to recognize any of the growth conditions. Analysis of the network weights reveals correlations between weighted combinations of peaks.
authors.affiliation: Center for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Lyngby. gorodkin@bioinf.au.dk
authors.forename: J
authors.initials: J
authors.lastname: Gorodkin
authors.forename: B
authors.initials: B
authors.lastname: Søgaard
authors.forename: H
authors.initials: H
authors.lastname: Bay
authors.forename: H
authors.initials: H
authors.lastname: Doll
authors.forename: P
authors.initials: P
authors.lastname: Kølster
authors.forename: S
authors.initials: S
authors.lastname: Brunak
mesh_terms: D002845:Chromatography / Q000379:methods; D002851:Chromatography, High Pressure Liquid; D005308:Fertilizers / Q000032:analysis; D005659:Fungicides, Industrial / Q000032:analysis; D001467:Hordeum / Q000737:chemistry* / Q000235:genetics* / Q000254:growth & development; D016571:Neural Networks, Computer; D009566:Nitrates / Q000032:analysis; D010636:Phenols / Q000737:chemistry*; D013045:Species Specificity
chemical_list: D005308:Fertilizers; D005659:Fungicides, Industrial; D009566:Nitrates; D010636:Phenols; C006568:ammonium nitrate