ANNUAL REPORT No.55 2004

I. CENTER FOR INFORMATION BIOLOGY AND DNA DATA BANK OF JAPAN
I-c. Laboratory for Gene Function Research - Yoshio Tateno Group

RESEARCH ACTIVITIES

(1) Submission of microarray data to public repositories

Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna-Assunta Sansone, Gavin Sherlock, Paul Spellman, Chris Stoeckert, Yoshio Tateno, Ronald Taylor, Joseph White and Neil Winegarden

--What this work states is a change in the way in which we approach the publication of microarray-based studies. Both authors and journals have a responsibility to assure that the requisite data are available, and because submitting MIAME-compliant data can take considerable time and effort, this process should be factored into review and publication timelines. However, while this process may be time consuming and painful at first, we believe that the benefits of building an open repository of microarray data will far outweigh any initial disadvantages. As always, it is our sincere hope that these suggestions stimulate discussion within the community and that together we can arrive at a consensus that ensures that microarray data are widely and easily accessible. Finally we would like to urge the DDBJ, EBI, and NCBI to work together towards exchanging all MIAME-compliant microarray data¹⁾.

(2) The origin of eukaryotes is suggested as the symbiosis of pyrococcus into proteobacteria by phylogenetic tree based on gene content

Tokumasa Horiike, Kazuo Hamada, Daisuke Miyata and Takao Shinozawa

--Attempts were made to define the relationship among the three domains (eukaryotes, archaea, and eubacteria) using phylogenetic tree analyses of 16S rRNA sequences as well as of other protein sequences. Since the results are inconsistent, it is implied that the eukaryotic genome has a chimeric structure. In our previous studies, the origin of eukaryotes to be the symbiosis of archaea into eubacteria using the whole open reading frames (ORF) of many genomes was suggested. In these studies, the species participating in the symbiosis were not clarified, and the effect of gene duplication after speciation (in-paralog) was not addressed. To avoid the influence of the in-paralog, we developed a new method to calculate orthologous ORFs. Furthermore, we separated eukaryotic in-paralogs into three groups by sequence similarity to archaea, eubacteria (other than -proteobacteria), and -proteobacteria and treated them as individual organisms. The relationship between the three ORF groups and the functional classification was clarified by this analysis. The introduction of this new method into the phylogenetic tree analysis of 66 organisms (4 eukaryotes, 13 archaea, and 49 eubacteria) based on gene content suggests the symbiosis of pyrococcus into -proteobacteria as the origin of eukaryotes²⁾.

(3) Integrative annotation of 21,037 human genes validated by full-length cDNA clones

Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, Roberto A. Barrero, Yoshio Tateno, Zhu Chen, Michio Oishi, Peter Tonellato, Rolf Apweiler, Kousaku Okubo, Lukas Wagner, Stefan Wiemann, Robert L. Strausberg, Takao Isogai, Charles Auffray, Nobuo Nomura, Takashi Gojobori and Sumio Sugano. et al.

--The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology³⁾.

(4) Structural and functional differences in two cyclic bacteriocins with the same sequences produced by lactobacilli

Yasushi Kawai, Yasuyuki Ishii, Kensuke Arakawa, Koichiro Uemura, Boku Saitoh, Junko Nishimura, Haruki Kitazawa, Yukiko Yamazaki, Yoshio Tateno, Takatoshi Itoh and Tadao Saito

--Lactobacillus gasseri LA39 and L. reuteri LA6 isolated from feces of the same human infant were found to produce similar cyclic bacteriocins (named gassericin A and reutericin 6, respectively) that cannot be distinguished by molecular weights or primary amino acid sequences. However, reutericin 6 has a narrower spectrum than gassericin A. In this study, gassericin A inhibited the growth of L. reuteri LA6, but reutericin 6 did not inhibit the growth of L. gasseri LA39. Both bacteriocins caused potassium ion efflux from indicator cells and liposomes, but the amounts of efflux and patterns of action were different. Although circular dichroism spectra of purified bacteriocins revealed that both antibacterial peptides are composed mainly of alpha-helices, the spectra of the bacteriocins did not coincide. The results of D- and L-amino acid composition analysis showed that two residues and one residue of D-Ala were detected among 18 Ala residues of gassericin A and reutericin 6, respectively. These findings suggest that the different D-alanine contents of the bacteriocins may cause the differences in modes of action, amounts of potassium ion efflux, and secondary structures. This is the first report that characteristics of native bacteriocins produced by wild lactobacillus strains having the same structural genes are influenced by a difference in D-amino acid contents in the molecules⁴⁾.

(5) Japanese domesticated chickens have been derived from Shamo traditional fighting cocks

Tomoyoshi Komiyama, Kazuho Ikeo, Yoshio Tateno and Takashi Gojobori

--With the aim of elucidating the evolutionary origin of Japanese domesticated chickens, this study evolutionarily analyzed 85 chicken mtDNA sequences. Thirty-four various ornamental chickens, 42 fighting cocks (Shamo), and nine long-crowing chickens (Naganakidori) were included. Of the Shamo, 18 were sampled from Okinawa, while the remaining 24 were collected in other islands around Japan. In addition, three Southeast Asian Junglefowls were used as a reference to determine the common ancestor of Japanese domesticated chickens. A phylogenetic tree was constructed for the 88 mtDNA sequences revealing that the Shamo group from Okinawa clearly diverged from the other Japanese domesticated chickens studied. This strongly suggests that all Japanese domesticated chickens, including the ornamental varieties and Naganakidori, derived from the ancestors of the Shamo in Okinawa. To create novel varieties of ornamental chickens, intensive artificial selection is imposed on ancestral Shamo populations, resulting in profoundly differentiated Japanese domesticated chickens⁵⁾.

(6) DDBJ in the stream of various biological data

Satoru Miyazaki, Hideaki Sugawara, Kazuho Ikeo, Takashi Gojobori and Yoshio Tateno

--In the past year we at DDBJ (http://www.ddbj.nig. ac.jp) have made a steady increase in the number of data submissions with a 50.6% increment in the number of bases or 46.5% increment in the number of entries. Among them the genome data of man, ascidian and rice hold the top three. Our activity has extended to providing a tool that enables sequence retrieval using regular expressions, and to launching our SOAP server and web services to facilitate the acquisition of proper data and tools from a huge number of biological data resources on websites worldwide. We have also opened our public gene expression database, CIBEX⁶⁾.

(7) Molecular chaperones: proposal of a systematic computer-oriented nomenclature and construction of a centralized database

Haitham Sghaier, Thuy Le Huyen Ai, Tokumasa Horiike and Takao Shinozawa

--Molecular chaperones are a wide group of unrelated protein families whose role is to assist others proteins. Comparably, under environmental stress, stress proteins behave as biocatalysts of protein stabilization. Stress proteins include a large class of proteins that were originally termed heat shock proteins (HSPs) due to their initial discovery in tissues exposed to elevated temperatures. Many, but not all, stress proteins and HSPs are molecular chaperones. Moreover, not all HSPs are derivable from stress. HSPs are structurally diversified by the contribution of various domains having specific roles. HSPs have been grouped, mainly on the basis of their molecular masses, into specific families that include small HSPs (sHSPs)/α-crystallins, HSP10s, HSP40s, HSP60s, HSP70s, HSP90s, HSP100s and HSP110s. The names of these major families are historical artefacts with limited information content. Using the current databases, names and proteic domains of many molecular chaperones in different species were analyzed. Although traditional names of HSPs are trivial, it is unrealistic to suggest replacing them, because they are preferred and widely used. Here we suggest that these traditional names be chaperoned, in silico, by a systematic nomenclature. Thus, for example, with the same intent of use of [trioxygen: O₃] for ozone, we propose here C7HSP70[Ehsa]ER-P11021 for GRP78 (78 kDa endoplasmic Human molecular chaperone in HSP70 superfamily with P11021 as its accession number in the database of the National Center for Biotechnology Information (NCBI)). The proposed systematic computer-oriented naming and classification method is designed for HSPs and also their partners based on the number of amino acids, domain structure, phylogenetic domain, localization in the cell and accession number as stated in the NCBI. Arabidopsis thaliana was analyzed as a model, because it contains a large number of various HSPs localized in several organelles. Overall, this naming system helps in building, optimizing and managing a novel online database entirely devoted to HSPs. The purported taxonomy, coupled with the newly constructed database, can contribute to studies involving large amounts of stored data on HSPs⁷⁾.

(8) Extensive analysis of ORF sequences from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock Identity of EST sequences between Haplochromis chilotes and Haplochromis sp. “Redtailsheller"

Masakatsu Watanabe, Naoki Kobayashi, Tadasu Shin-I, Tokumasa Horiike, Yoshio Tateno, Yuji Kohara and Norihiro Okada

--The Lake Victoria Cichlid fishes have diverged very rapidly. The estimated 500 species inhabiting the lake are believed to have arisen within the last 14,000 years. The fishes' jaws and teeth have diverged markedly to adapt to different feeding behaviors and environments. To examine how the genomes of these fishes differentiated during speciation, we performed comparative analysis of expressed sequenced tag (EST) sequences. We constructed cDNA libraries derived only from the jaw portions of two cichlid species endemic to Lake Victoria. We sequenced 17,280 cDNA clones from Haplochromis chilotes and 9600 cDNA clones from Haplochromis sp. “Redtailsheller" and obtained 543 different genes common to both species. Of these genes, 441 were essentially identical between species and 102 contained base replacements in their open reading frame (ORF) or untranslated (UTR) regions. Comparative analysis of 71selected sequences has revealed that while the degree of polymorphism is 0.0054/site for H. chilotes and 0.0047/site for H. sp. “Redtailsheller", genetic distance between the two species is 0.0031/site. The genetic distance particularly indicates that the two species diverged about 890,000 years ago⁸⁾.

(9) International public gene expression database (CIBEX) and data submission

Yoshio Tateno and Kazuho Ikeo

--We have opened our gene expression database, CIBEX, to the public. CIBEX has been developed as an international public database with the aim of the collaboration with ArrayExpress at EBI and GEO at NCBI. The collaboration mainly means to share the annotation manual and to exchange the data collected and annotated among the three databases. The data collection will hopefully be promoted by the open letter issued by the MGED society to the editors of relevant journals⁹⁾.

(10) Analysis of biological networks in eukaryotes using the whole genome sequences

Tsuyoshi Tanaka and Takashi Gojobori

--Since the whole genome sequencing of Haemophilus influenzae was completed in 1995, the number of species whose genomes were completely sequenced has steeply been increased. As of January 2005, the number of such species is more than 210 in the Genome Information Broker (GIB) of the Center for Information Biology and DNA Data Bank of Japan. The information on the whole genome sequences enables us to study the origins and evolutionary processes of various biological networks such as metabolic pathways and signal transductions. We analyzed biological networks such as amino acid metabolic pathways by conducting comparative analysis of the complete genome sequences of six eukaryotic species including man, fly, nematode, yeasts and plant, and found that a particular pathway had evolved independently in multiple lineages of the species studied¹⁰⁾.

(11) Microarray gene expression database

Kazuho Ikeo and Yoshio Tateno

--As the international standardizations of microarray data description and data sharing have been promoted by the MGED society, researchers conducting microarray experiments are encouraged to submit their data to one of the international gene expression databases, ArrayEpress, GEO and CIBEX. CIBEX being developed by us is in compliance with the international standard, MIAME, and equipped with several search functions¹¹⁾.

(12) Discovery and annotation of forty seven non-protein coding human RNAs

Roberto A. Barrero, Inna Dubchak, Charles Auffray, Laurens Wilming, Jun-ichi Takeda, Yutaka Suzuki, Erimi Harada, Marie-Anne Debily, Esther Graudens, John Quackenbush, Takuro Tamura, Dmitriy V. Ryaboy, Sandrine Imbeaud, Kazuho Ikeo, Peter Tonellato, Nobuo Nomura, Sumio Sugano, Tadashi Imanishi, Takashi Gojobori and Libin Jia

--Non-coding RNAs (ncRNAs) play crucial roles in a variety of procsses including replication, transcriptional regulation, splicing, dosage compensation, genetic imprinting, translational regulation, and modulation of protein function. Here we report the discovery and annotation of ncRNAs from the human full-length cDNA dataset evaluated at the first International Human Full-length cDNA Annotation Meeting. A total of 1,485 cDNA transcripts, mapped onto 1,300 loci on the human genome, were found to encode putative open reading frames (ORFs) equal to or less than 80 amino acids (aa). To select putative ncRNAs all cDNA sequences were mapped to the human genome to study the genomic neighbourhood for the presence of ab initio predicted genes and neighbouring genes, and compared to Expressed Sequence Tag (EST) databases for supporting evidence. This method yielded 296 putative ncRNAs that were analyzed for conservation by determining mouse DNA and RNA sequence similarities. Putative ncRNAs with mouse ortholog support were further analyzed using QRNA. We found 47 ncRNAs containing a conserved RNA secondary structure. Of these, 60% were found to be expressed in up to eight human tissues, implying that ncRNAs are seemingly tissue-specifically regulated.

(13) Evolutionary rate of enzymes in the metabolic network

Tsuyoshi Tanaka, Kazuho Ikeo and Takashi Gojobori

--An enzyme interacts not only with the other proteins but also with low-weight molecules called substrates in the metabolic network. To understand an evolutionary process of interactions of enzymes, we studied the relationship between the evolutionary rate of the enzyme and these interacting partners. When we focused on the 498 enzymes in Saccharomyces cerevisiae that have orthologous pairs in Ashbya gossypii, we discovered the significant negative correlation between the evolutionary rate of the enzyme and the number of interacting proteins (protein-protein interaction; PPI). On the other hand, we found no correlation between the evolutionary rate of the enzyme and the number of interacting substrates (protein-substrate interaction; PSI). Therefore, we conclude that the number of interacting proteins is the most affective to the evolutionary rate of the enzyme compared with that of the other interacting partners such as the substrates.

(14) Development of a method for constructing a phylogenetic tree using a comprehensive orthologous gene cluster, and phylogenetic analysis of cyanobacteria

Tokumasa Horiike and Yoshio Tateno

--Phylogenetic trees are constructed using DNA, RNA or amino acid sequences for estimating evolutionary relationships of genes or species. Currently, there are two problems with the tree construction. One is that horizontal gene transfer disturbs the estimation of the true relationships of genes or species. The other is that the construction sometimes depends on the choice of sequences. We occasionally observe that changing one sequence to another erroneously alters the reconstructed tree. Therefore, we are developing a method of the tree construction which is to reduce the interference caused by the two problems. In the method we can incorporate all available prokaryotic ORFs. We will then clarify the phylogenetic position of cyanobacteria by applying our method to as many pertinent sequences as possible.

(15) We are in collaboration with Prof. Tadao Saito of Tohoku University and his laboratory on the function and evolution of glucosidase and galactosidase genes in Lactobcillus

Tadao Saito, Yukiko Yamazaki and Yoshio Tateno

(16) We are in collaboration with Prof. Shintou Eguchi of the Institute of Mathematical Statistics and his laboratory on the statistical analyses of SNP and gene expression data

Shinto Eguchi, Kazuho Ikeo and Yoshio Tateno

PUBLICATIONS

Papers
1. Ball, CA., Brazma, A., Causton, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, JC., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, SA., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J. and Winegarden, N. (2004). Submission of microarray data to public repositories. PLoS Biol. 2, 1276-1277, also Microbiology 150, 3522-3524 and Environ Health Perspect 112, A666-A667.
2. Horiike, T., Hamada, K., Miyata, D. and Shinozawa, T. (2004). The origin of eukaryotes is suggested as the symbiosis of pyrococcus into γ-proteobacteria by phylogenetic tree based on gene content. J. Mol. Evol. 59, 606-619.
3. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, KO., Barrero, RA., Tateno, Y., Chen, Z., Oishi, M., Tonellato, P., Apweiler, R., Okubo, K., Wagner, L., Wiemann, S., Strausberg, RL., Isogai, T., Auffray, C., Nomura, N., Gojobori, T. and Sugano, S. et al. (2004). Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2, 256-275.
4. Kawai, Y., Ishii, Y., Arakawa, K., Uemura, K., Saitoh, B., Nishimura, J., Kitazawa, H., Yamazaki, Y., Tateno, Y., Itoh, T. and Saito, T. (2004). Structural and functional differences in two cyclic bacteriocins with the same sequences produced by lactobacilli. Appl Environ Microbiol. 70, 2906-2911.
5. Komiyama, T., Ikeo, K., Tateno, Y. and Gojobori, T. (2004). Japanese domesticated chickens have been derived from Shamo traditional fighting cocks. Mol Phylogenet Evol. 33, 16-21.
6. Miyazaki, S., Sugawara, H., Ikeo, K., Gojobori, T. and Tateno, Y. (2004). DDBJ in the stream of various biological data. Nucleic Acids Res. 32, D31-D34.
7. Sghaier, H., Ai, TL., Horiike, T. and Shinozawa, T. (2004). Molecular chaperones: proposal of a systematic computer-oriented nomenclature and construction of a centralized database. In Silico Biol. 16, 0025.
8. Watanabe, M., Kobayashi, N., Shin-I, T., Horiike, T., Tateno, Y., Kohara, Y. and Okada, N. (2004). Extensive analysis of ORF sequences from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock Identity of EST sequences between Haplochromis chilotes and Haplochromis sp. “Redtailsheller". Gene 343, 263-269.
9. 舘野義男,池尾一穂（2004）国際公共遺伝子発現データベース（CIBEX）とデータの登録,蛋白質核酸酵素49, 2679-2683.
10. 田中剛,五條堀孝（2004）ゲノムの比較解析と分子進化,生体の科学55, 241-246.
11. 池尾一穂,舘野義男（2004）マイクロアレイ遺伝子発現データベース,ゲノミックスプロテオミックスの新展開（今中忠行監修）,pp828-836,NTS出版.

Database
12. DDBJ is operated by DNA Data Analysis, Gene Function Research, Gene-Product Informatics, Research and Development of Biological Databases and Gene Expression Laboratories, and Division of Population Genetics. DDBJ collects, annotates and publishes DNA sequence data, and exchanges the data with EMBL Bank and GenBank on a daily basis. In addition, DDBJ edits the data published by DDBJ, EMBL Bank and GenBank together four times a year and publishes as a release. In 2004 DDBJ published the following four releases.

Release 57 March., 04

32,693,678 entries

38,008,449,840 bases

Release 58 June., 04

34,917,581 entries

39,812,635,108 bases

Release 59 Sept., 04

37,926,117 entries

44,416,752,273 bases

Release 60 Dec., 04

40,583,945 entries

42,245,956,937 bases

13. Dr. Y. Tateno attended the 17^th International Nucleotide Sequence Databases Collaborative Meeting, and the 15^th International Nucleotide Sequence Databases Advisors Meeting held at EBI, Hinxton, UK, May, 2004.
14. Dr. Y. Tateno attended the MGED Board Meeting, Toronto, Canada, September, 2004.
15. Dr. Y. Tateno was invited to be a chairperson of a session at the UniProt Meeting, Antibes, France, September, 2004.

ORAL PRESENTATIONS

1. Tateno, Y. "International standardization of microarray data and our microarray database, CIBEX" A-IMBN/EMBO Workshop, Tokyo, March, 2004.
2. Horiike T. Origin of eukaryotic cell nuclei by symbiosis of archaea in eubacteria supported by whole protein data analysis. Lateral Gene transfer and the origins of eukaryotes, Harrison Hot Springs Resort, Canada, May, 2004.
3. Barrero R.A. Evolution of mammalian microRNAs and their regulatory targets. 6^th Japanese Society of Evolution, Tokyo, August, 2004.
4. Tateno, Y., Ikeo, K., Hayashizaki, Y. "CIBEX and data standardization" The 7^th MGED Society Meeting, Toronto, Canada, September, 2004.
5. Tateno, Y. "DNA Data Bank of Japan and the H-Invitational" KISTI, Deajeon, Korea, November, 2004.
6. Barrero R.A. Evolution of microRNA genes and their targets. 5^th HUGO Pacific Meeting & 6^th Asia-Pacific Conference on Human Genetics, Singapore, November, 2004.
7. Tateno, Y. "Genomic evolution of MHC class I regions in primates." The 2^nd Mishima Workshop, Hakone, November, 2004.
8. 舘野義男「遺伝子情報解析の現況」スーパーSINET推進協議会、東京、2004年5月
9. 舘野義男、池尾一穂「マイクロアレイデータの標準化と遺伝子発現データベース（CIBEX）」第42回生物物理学会、京都、2004年12月

POSTER PRESENTATIONS

1. Barrero, R.A., Auffray, C., Suzuki, Y., Dubchak, I., Wilming, L., Sugano, S., Imanishi, T., Gojobori, T., and Jia, L. "Discovery and annotation of non-protein coding human RNAs". HUGO 2004: Human Genome Meeting, Berlin, Germany, April, 2004.
2. Tanaka T, Tateno Y, Gojobori T. Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Genomes and Evolution 2004, Pennsylvania, U.S.A., June, 2004.
3. Barrero, R.A., Tamura, T., Sakurai, H., Hayakawa, S., Tateno, Y., Ikeo, K., Imanishi, T. and Gojobori, T. "Evolution of mammalian microRNA genes and their regulatory targets". Beyond the Identification of Transcribed Sequences: Functional, Expression and Evolutionary Analysis,14th International Workshop, Kazusa, Chiba, October, 2004.
4. Hayakawa, S, Barrero, R.A., Sakurai, H., Tamura, T.,Tateno, Y., Ikeo, K., Imanishi, T. and Gojobori,T. Computational prediction of novel mammalian microRNAs. 27th Annual Meeting of the Molecular Biology Society of Japan, Kobe, December, 2004.
5. Barrero, R.A., Tamura, T., Sakurai, H., Hayakawa, S.,Tateno,Y., Ikeo, K., Imanishi, T. and Gojobori, T. microRNAs: biology and evolution. 27th Annual Meeting of the Molecular Biology Society of Japan, Kobe, December, 2004.
6. Zhang, H., Barrero, R.A., Harada, E., Tamura, T., Gojobori, T. and Imanishi, T. "ANFA: A Computacional Annotation System for Non-Protein Coding Transcripts". 27th Annual Meeting of the Molecular Biology Society of Japan, Kobe, December, 2004.
7. Barrero, R.A., Tamura, T., Sakurai, H., Hayakawa, S., Tateno, Y., Ikeo, K., Imanishi, T. and Gojobori, T. "microRNAs: biology and evolution". 27th Annual Meeting of the Molecular Biology Society of Japan, Kobe, December, 2004.
8. Hayakawa, S., Barrero, R.A., Sakurai, H., Tamura, T., Tateno, Y., Ikeo, K., Imanishi, T. and Gojobori, T. "Computational prediction of novel mammalian miRNAs". 27th Annual Meeting of the Molecular Biology Society of Japan, Kobe, December, 2004.
9. Toshihisa Okido, Yasumasa Shigemoto, Masashi Matsuo, Tadashi Koike, Satoshi Fukuchi, Tadashi Imanishi, Satoru Miyazaki, Yoshio Tateno, Takashi Gojobori. Construction of H-Invitational Database CIB-DDBJ Flat File Server. The 15th International Conference on Genome Informatics, Yokohama, December, 2004.
10. 大城戸利久、重元康昌、松尾昌嗣、小池匡、福地佐斗志、今西規、宮崎智、舘野義男、五條堀孝「H-Invitational Database CIB-DDBJ Flat File Serverの構築」第27回日本分子生物学会、神戸市、2004年12月
11. 櫻井仁美、Roberto Barrero、早川志帆、田村卓郎、舘野義男、池尾一穂、今西規,五條堀孝「哺乳類マイクロRNA (miRNA)の標的遺伝子予測と実験的検証」第27回日本分子生物学会、神戸市、2004年12月
12. 松村米浩、下川和郎、河合純、池尾一穂、舘野義男、林崎良英「DNAマイクロアレイデータに対するスポット単位の信頼性指標の開発と、READデータへの信頼性指標の付与」第27回日本分子生物学会、神戸市、2004年12月
13. 櫻井仁美、R.A. Barrero、早川志帆、田村卓郎、舘野義男、池尾一穂、今西規、五條堀孝「哺乳類マイクロRNA (miRNA)の標的遺伝子予測と実験的検証、第27回日本分子生物学会年会、神戸市、2005年12月
14. 原田えりみ、R.A. Barrero、武田淳一、C. Auffray、鈴木穣、I. Dubchak、L. Wilming、菅野純夫、今西規、五條堀孝「ヒト完全長cDNAからの機能性RNA候補の検出と機能解析、第27回日本分子生物学会年会、神戸市、2005年12月
15. 今西規、藤井康之、山崎千里、伊藤剛、小柳香奈子、R.A.. Barrero、田村卓郎、山口由美、谷野元彦、武田淳一、野村信夫、菅野純夫、五條堀孝「ヒト遺伝子の統合アノテーションテータべース:H-Invitational Database、第27回日本分子生物学会年会、神戸市、2005年12月
16. 田中進、谷家貴之、花岡秀樹、前川陽俊、山崎千里、R.A. Barrero、B. Lenhard、M. Data、M. Shimoyama、今西規、五條堀孝「新規疾病感受性遺伝子予測のためデータマイニングシズテムの構築、第27回日本分子生物学会年会、神戸市、2005年12月
17. 田中剛、池尾一穂、五條堀孝、代謝ネットワークにおける酵素の進化速度の解析、第27回日本分子生物学会年会、神戸市、2004
18. 堀池徳祐、濱田一男、宮田大輔、篠沢隆雄、真核生物の起源:オルソロガス遺伝子を元に作成した系統樹による推定、第27回日本分子生物学会年会、神戸市、2004

EDUCATION

1. Dr. Y. Tateno co-organized the 3rd Japan-Korea Bioinformatics Training Course at NIG, March, 2004.
2. Dr. Y. Tateno co-organized the SOKENDAI international lecture and gave a lecture on DNA and Protein Databases at the Olympic Hotel, Shanghai, China, October, 2004.

SOCIAL CONTRIBUTIONS AND OTHERS

学会活動
1. Dr. Y. Tateno serves the Microarray Gene Expression Data Society as an Advisory Board Member (2001-), and attended the Board Member Meeting, Toronto, Canada, September, 2004.
2. Dr. Y. Tateno serves the Society of Evolutionary Studies as a Member of the Committee of Genetics under the Science Council of Japan.
3. Dr. Y. Tateno serves the Genetics Society of Japan as a Member of Editorial Boar