GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data

Background: One-dimensional (1-D) electrophoretic data obtained using the cDNA-AFLP method have attracted great interest for the identification of differentially expressed transcriptderived fragments (TDFs). However, high-throughput analysis of the cDNA-AFLP data is currently limited by the need for labor-intensive visual evaluation of multiple electropherograms. We would like to have high-throughput ways of identifying such TDFs. Results: We describe a method, GOGOT, which automatically detects the differentially expressed TDFs in a set of time-course electropherograms. Analysis by GOGOT is conducted as follows: correction of fragment lengths of TDFs, alignment of identical TDFs across different electropherograms, normalization of peak heights, and identification of differentially expressed TDFs using a special statistic. The output of the analysis is a highly reduced list of differentially expressed TDFs. Visual evaluation confirmed that the peak alignment was performed perfectly fo...

• Type: Journal
• Year: 2007
• Where: ALMOB
• Authors: Koji Kadota, Ryoko Araki, Yuji Nakai, Masumi Abe
• Keywords: ALMOB 2007, Electrophoretic Data, Labor-intensive Visual Evaluation, Visual Evaluation