*** 第178回 CBI研究講演会 ***

「Genes and Genomes」

3月16日の講演会と開催日が近くなってしまいましたが、 BioInformatics分野の専門家が時を同じくして来日されるので講演会を企画しました。 Dr. Peer Borkは、ここ数年ゲノム情報から機能情報を引き出すための研究成果を次々と出しておられますが、ここでは二つのテーマで話をしてもらうことにしました。最初は最近のこの分野の動向や問題点を総括したレビューであり、次は最近彼のグループで行った比較ゲノミックスに関するいくつかの研究成果の紹介です。 ロシアのBioInformatics分野のリーダーの一人であるProf. Nikolay A. Kolchanovには、彼のグループで開発した“GeneExpres”システムの紹介をして頂きます。これは遺伝子発現制御に関する増大しつつある情報をデータベースに蓄積し、そこから有用な知識を抽出するシステムで、転写制御領域や機能部位の解析・予測の機能を有しています。いずれも非常にホットな話題ですのでぜひ御参加下さい。

日時: 1999年3月19日(金) 13:30-17:00

場所: 化学会館６階大会議室
東京都千代田区神田駿河台1-5 (JRお茶の水駅下車、徒歩4分)

世話人：八尾 徹(理化学研究所)、中田琴子(国立医薬品食品衛生研究所)

演題:
1．13:30-15:50
Dr. Peer Bork (EMBL, Germany)

(1) "Predicting Biology from Sequence: Where are the bottlenecks ? "
講演要旨
The exponential growth of sequence data does not necessarily lead to an increase in knowledge about the functions of genes and their products. Prediction of function [1] and structure [2] based on homology is extremely powerful, but, if not performed appropriately, may also lead to the creation and propagation of assignment errors. Various levels of sequence annotation and function prediction, from domain identification [3] to pathways analysis, are discussed, considering also the added value of completely sequenced genomes (e.g. [4]).

[1] Bork,P. & Koonin,E.V. (1998). Predicting function from protein sequences: Where are the bottlenecks?. Nature Genet., 18, 313-318
[2] Huynen,M.A., Doerks,T., Eisenhaber,F., Orengo,C., Sunyaev,S.R., Yuan,Y.P. & Bork,P. (1998). Homology-based fold predictions for Mycoplasma genitalium proteins. J.Mol.Biol., 280, 323-326
[3] Schultz,J., Milpetz,F., Bork,P. & Ponting,C.P. (1998). SMART, a simple modular architecture research tool: Identification of signaling domains. PNAS, 95, 5857-5864
[4] Huynen,M.A., Diaz-Lazcoz,Y. & Bork,P. (1997). Differential genome display. Trends Genet., 13, 389-390

(2) "Comparing Genes and Genomes: From Polymorphism to Phylogeney"
講演要旨
Applications of comparative methods at several levels are presented. Depending on the phylogenetic distance of genes or genomes, different types of information can be extracted [1]. For example, computational methods are successfull in the prediction of polymorphism within species and the challenge is to discriminate true variation from sequencing errors. Samples from more than 600 individuals are stored in EST databases i.e. many more than accessable in current experiments. A comparative method for the prediction of human polymorphism in coding regions is applied to disease-accosiated genes. While the study of human diversity obviously requires very similar sequences, information from distant relationships can be used for structural and functional predictions. The advent of completely sequenced genomes allows to address qualitatively new questions and put forward solutions at a higher level [2]. For example, shared gene content decreases with the phylogenetic distance between species [1] and indeed neighbor-joining trees with shared gene content as a distance criterion fit surprisingly well to "standard" ones derived from 16s RNA sequences [3]. Thus, the method seems to overcome conflicting results derived from distinct molecules. The observed tree also indicates that the effect of horizontal gene transfer on gene content is surprisingly small.

[1] Huynen,M.A. & Bork,P. (1998). Measuring genome evolution. PNAS, 95, 5849-5856
[2] Bork,P., Dandekar,T., Diaz-Lazcoz,Y., Eisenhaber,F., Huynen,M.A. & Yuan,Y.P. (1998).Predicting function: From genes to genomes and back. J.Mol.Biol., 283, 707-725
[3] Snel,B., Bork,P. & Huynen,M. (1999). Genome phylogeny based on gene content. Nature Genet, 21, 108-110

2．16:00-17:00
Prof. N.A.Kolchanov (Institute of Cytology and Genetics, Russia)

"Gene Express: Intelligent system on gene expression regulation"
講演要旨
Nikolay A Kolchanov(The Institute of Cytology and Genetics, Russia) The goal of the work was to develop an WWW-oriented computer system providing a maximal integration of informational and software resources on regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. Results. The GeneExpress system, including the following major informational and software modules, has been developed: (1) Transcription Regulation module, which contains the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD viewer for data visualization; (2) Transcription Factor Binding Site Recognition module, which comprises (a) the B-DNA-VIDEO system for detecting the conformational and physico-chemical properties of DNA sites significant for their recognition, (b) the ConsFrec system for detecting significant context properties of sites and their recognition, and (c) the system for detecting significant conservative regions of functional sites and their recognition; (3) ACTIVITY, the module for analysis of functional site activity and its prediction; (4) GeneNet, including an object-oriented database accumulating the data on gene networks and signal transduction pathways and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation, designed for analyzing structural and contextual properties of mRNA 5'UTRs and predicting their translation efficiency; and (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins.
講演会参加資格：CBI研究会個人会員・法人会員の方、非営利研究機関の研究者の方は、どなたでも参加できます。法人会員以外の法人からの参加希望者は、一人 3000円の参加費が必要です。会場準備の都合がありますので、参加される方は事前に事務局にご連絡ください。

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