@article{oai:repo.qst.go.jp:00044672,
 author = {Kadota, Koji and Fukumura, Ryuutarou and John, Rodrigue Joseph and Araki, Ryoko and Abe, Masumi and 門田 幸二 and 福村 龍太郎 and Ｊｏｓｅｐｈ Ｊｏｈｎ Ｒｏｄｒｉｇｕｅ and 荒木 良子 and 安倍 真澄},
 issue = {1},
 journal = {BMC Bioinformatics (online only URL:http://www.biomedcentral.com/bmcbioinformatics)},
 month = {Mar},
 note = {BACKGROUND: Gene expression analysis based on comparison of electrophoretic
patterns is strongly dependent on the accuracy of DNA fragment sizing. The
current normalization strategy based on molecular weight markers has limited
accuracy because marker peaks are often masked by intense peaks nearby.
Cumulative errors in fragment lengths cause problems in the alignment of
same-length fragments across different electropherograms, especially for
small fragments (< 100 bp). For accurate comparison of electrophoretic
patterns, further inspection and normalization of electrophoretic data after
fragment sizing by conventional strategies is needed. RESULTS: Here we
describe a method for the normalization of a set of time-course
electrophoretic data to be compared. The method uses Gaussian curves fitted
to the complex peak mixtures in each electropherogram. It searches for
target ranges for which patterns are dissimilar to the other patterns
(called "dissimilar ranges") and for references (a kind of mean or typical
pattern) in the set of resultant approximate patterns. It then constructs
the optimal normalized pattern whose correlation coefficient against the
reference in the range achieves the highest value among various combinations
of candidates. We applied the procedure to time-course electrophoretic data
produced by HiCEP, an AFLP-based expression profiling method which can
detect a slight expression change in DNA fragments. We obtained dissimilar
ranges whose electrophoretic patterns were obviously different from the
reference and as expected, most of the fragments in the detected ranges were
short (< 100 bp). The normalized electrophoretic patterns also agreed well
with reference patterns. CONCLUSION: The normalization strategy presented
here demonstrates the importance of pre-processing before electrophoretic
signal comparison, and we anticipate its usefulness especially for temporal
expression analysis by the electrophoretic method.},
 pages = {43--57},
 title = {A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: toward the strict alignment of valid fragments across electrophoretic patterns.},
 volume = {6},
 year = {2005}
}