tailieunhanh - Báo cáo sinh học: "GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data. | Algorithms for Molecular Biology BioMed Central Research Open Access GOGOT a method for the identification of differentially expressed fragments from cDNA-AFLP data Koji Kadota1 Ryoko Araki2 Yuji Nakai1 and Masumi Abe 2 Address Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan and 2Transcriptome Research Center National Institute of Radiological Sciences NIRS 9-1 Anagawa-4-chome Chiba-shi 263-8555 Japan Email Koji Kadota - kadota@ Ryoko Araki - a_ryo@ Yuji Nakai - yunakai@ Masumi Abe - abemasum@ Corresponding author Published 30 May 2007 Received 6 February 2007 Algorithms for Molecular Biology 2007 2 5 doi 1748-7188-2-5 Accepted 30 May 2007 This article is available from http content 2 1 5 2007 Kadota et al licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Background One-dimensional 1-D electrophoretic data obtained using the cDNA-AFLP method have attracted great interest for the identification of differentially expressed transcript-derived 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 .