Automated pattern ranking in differential display data analysis.
Gene expression analysis by differential display (DD) is limited by the labor-intensive visual evaluation of the electrophoretic data traces. We describe a flexible method for computer-assisted ranking of expression patterns in data from DD experiments. The method is based on a pairwise alignment and comparison of the quantitative trace data with respect to specific expression patterns defined by the investigator. The observed patterns are ranked according to a score value that identifies the most potential findings to be confirmed visually instead of the vast amount of original results. This two-step approach, enabled by the efficient computer algorithm for gene expression pattern comparison, will increase the percentage of true-positive findings chosen for the tedious downstream processing, while minimizing the cost and labor involved in large scale DD data analysis.
Aittokallio
Tero
T
Department of Mathematics and TUCS, University of Turku, Finland.
Ojala
Pekka
P
Nevalainen
Timo J
TJ
Nevalainen
Olli S
OS
D000465:Algorithms; D001331:Automation; D045744:Cell Line, Tumor; D019295:Computational Biology; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism; D003627:Data Interpretation, Statistical; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D012333:RNA, Messenger / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012984:Software
D017931:DNA Primers; D018076:DNA, Complementary; D012333:RNA, Messenger