Genome Informatics 11: 264–265 (2000)
264
A Web Based System for Computation and Management of Massive Number of 2-D Gel Electrophoretograms of Genomic DNA Katsutoshi Takahashi1
Masayuki Nakazawa2
[email protected]
[email protected]
Yasuo
Watanabe3
[email protected] 1 2 3
Akihiko Konagaya3
[email protected]
Japan Advanced Institute of Science and Technology (JAIST) Hokuriku, Asahidai 1-1, Tatsunokuchi, Ishikawa 923-1211, Japan Kanazawa Technical College, Hisayasu 2-270, Kanazawa, Ishikawa 921-8601, Japan Kanazawa Institute of Technology, Ohgigaoka 7-1, Nonoichi, Ishikawa 921-8501, Japan
Keywords: RLGS, 2-D gel electrophoresis, spot recognition, spot pattern matching, web based analysis
1
Introduction
DNA methylation occurring within the context of CpG site in the promoter element generally correlates with transcriptional silencing, delayed replication and condensed chromatin [1]. Recently, it was reported that CpG-islands of several tumor-suppressor gene promoters were hypermethylated in tumor and there were tumor-type-specific hypermethylation patterns [3]. It is also strongly suggested that DNA methylation correlates to mammalian genome imprinting. Restriction landmark genomic scanning (RLGS) method [2] is one of the most powerful strategies which profiles methylation status of several thousands of CpG-islands across the genome. In RLGS method, NotI endnuclease recognition sites are imaged as several thousands of landmark spots on RLGS electrophoretogram (RLGS profile). The DNA methylation or gene amplification changes can be emerged by comparing several related RLGS profiles. It is difficult, however, by visual inspection to detect the locations and intensities of the RLGS landmark spots from the RLGS profile and to compare them rapidly and objectively. Thus, the computer-assisted analysis of the RLGS profile is necessary. Besides, RLGS profiles should be processed by computer without any human interaction, in order to manage large amount of RLGS profiles and to retrieve DNA methylation status of the CpG islands. In this poster, a web based system “WebDNAinsight”, in which the fully-automated RLGS image processing algorithms [4] are integrated with the powerful image database, is presented. With the web interface, one can register, search, process and analyze massive number of RLGS profiles easily, using networked computer with web browser.
2
System Overview
The WebDNAinsight system has been designed to work collaborating with a web server. With such web based interface, one can easily register RLGS profile images into WebDNAinsight image database, search and choose the images from the database using networked computer that has web browser. The request for the automated spot recognition or spot matching computations can be made against the web server via web browser. The WebDNAinsight system automatically schedules each computational request and processes all of them in background.
Computation of 2-D Gel Electrophoretograms
265
Figure 1: Snapshot of WebDNAinsight web interface.
Once the requested task is processed, characteristics of the all identified spots or the spots which have changed their intensities among several related RLGS profiles can be retrieved and displayed on the web browser as shown in Figure 1.
3
Acknowledgement
We are grateful to Prof. Ueda at Keio University for providing RLGS autoradiogram images. This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas ‘Genome Science’ from The Ministry of Education, Science, Sports and Culture of Japan.
References [1] Charis, E., James, G.H., and Stephen B.B., A bird’s eye view of global methylation, Nature Genetics, 24:101–102, 2000. [2] Hatada, I., Hayashizaki, Y., Hirotsune, S., Komatsubara, H., and Mukai, T., A genomic scanning method for higher organisms using restriction sites as landmarks, Proc. Natl. Acad. Sci. USA, 88:9523–9527, 1991. [3] Joseph F.C., Michael, C.F., et al., Aberrant CpG-island methylation has non-random and tumourtype-specific patterns, Nature Genetics, 24:132–138, 2000. [4] Takahashi, K., Nakazawa, M., Watanabe, Y., and Konagaya, A., Automated processing of 2-D gel electrophoretograms of genomic DNA for hunting pathogenic DNA molecular changes, Genome Informatics, 10:121–132, 1999.
