K Nakai

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. pmc Profiling ascidian promoters as the primordial type of vertebrate promoter
    Kohji Okamura
    Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    BMC Genomics 12:S7. 2011
  2. pmc Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin
    Yoshiaki Tanaka
    Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
    Chromosoma 119:391-404. 2010
  3. pmc PrognoScan: a new database for meta-analysis of the prognostic value of genes
    Hideaki Mizuno
    Pharmaceutical Technology Department, Kamakura Research Laboratories, Chugai Pharmaceutical Co Ltd, Kamakura, Kanagawa, Japan
    BMC Med Genomics 2:18. 2009
  4. pmc Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
    BMC Genomics 11:S1. 2010
  5. pmc Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
    Hirokazu Chiba
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    BMC Genomics 9:152. 2008
  6. pmc Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions
    Katsuhiko Murakami
    Integrated Database Group, Japan Biological Information Research Center JBIRC, Japan Biological Informatics Consortium, Aomi 2 41, Koto ku, Tokyo, 135 0064, Japan
    BMC Genomics 9:112. 2008
  7. pmc Effects of Alu elements on global nucleosome positioning in the human genome
    Yoshiaki Tanaka
    Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
    BMC Genomics 11:309. 2010
  8. pmc A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns
    Sung Joon Park
    Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    BMC Bioinformatics 12:S50. 2011
  9. pmc Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution
    Kohji Okamura
    Human Genome Centre, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato Ward, Tokyo 108 8639, Japan
    BMC Bioinformatics 11:S2. 2010
  10. pmc Genome informatics for data-driven biology
    Kenta Nakai
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Genome Biol 3:REPORTS4010. 2002

Detail Information

Publications59

  1. pmc Profiling ascidian promoters as the primordial type of vertebrate promoter
    Kohji Okamura
    Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    BMC Genomics 12:S7. 2011
    ..However, the limited annotation of these genes has impeded the large-scale analysis of their promoters...
  2. pmc Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin
    Yoshiaki Tanaka
    Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
    Chromosoma 119:391-404. 2010
    ..Furthermore, the associations with gene function and histone modification were also discussed here...
  3. pmc PrognoScan: a new database for meta-analysis of the prognostic value of genes
    Hideaki Mizuno
    Pharmaceutical Technology Department, Kamakura Research Laboratories, Chugai Pharmaceutical Co Ltd, Kamakura, Kanagawa, Japan
    BMC Med Genomics 2:18. 2009
    ..The database is publicly accessible at http://gibk21.bse.kyutech.ac.jp/PrognoScan/index.html...
  4. pmc Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
    BMC Genomics 11:S1. 2010
    ..27 - Dec. 2, 2011 at Kuala Lumpur, Malaysia...
  5. pmc Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
    Hirokazu Chiba
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    BMC Genomics 9:152. 2008
    ..A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial...
  6. pmc Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions
    Katsuhiko Murakami
    Integrated Database Group, Japan Biological Information Research Center JBIRC, Japan Biological Informatics Consortium, Aomi 2 41, Koto ku, Tokyo, 135 0064, Japan
    BMC Genomics 9:112. 2008
    ..It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and their positional distribution...
  7. pmc Effects of Alu elements on global nucleosome positioning in the human genome
    Yoshiaki Tanaka
    Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
    BMC Genomics 11:309. 2010
    ..As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still unclear whether this feature can be observed in the whole genomes of all eukaryotes...
  8. pmc A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns
    Sung Joon Park
    Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    BMC Bioinformatics 12:S50. 2011
    ..In it, the role of several core transcription factors (TFs), such as Oct4, Sox2 and Nanog, has been intensively investigated, details of their involvement in the genome-wide gene regulation are still not well clarified...
  9. pmc Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution
    Kohji Okamura
    Human Genome Centre, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato Ward, Tokyo 108 8639, Japan
    BMC Bioinformatics 11:S2. 2010
    ..However, DNA methylation patterns and levels in vertebrates and invertebrates have not been analyzed in the same way...
  10. pmc Genome informatics for data-driven biology
    Kenta Nakai
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Genome Biol 3:REPORTS4010. 2002
  11. ncbi request reprint [Tell me about algorithms in bioinformatics, Dr. Ochanomizu]
    Kenta Nakai
    Tanpakushitsu Kakusan Koso 47:1332-6. 2002
  12. pmc Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species
    G Terai
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Genome Biol 2:RESEARCH0048. 2001
    ..To overcome this problem, we used conserved information from three closely related species: Bacillus subtilis, B. halodurans and B. stearothermophilus...
  13. pmc DBTSS provides a tissue specific dynamic view of Transcription Start Sites
    Riu Yamashita
    Frontier Research Initiative, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
    Nucleic Acids Res 38:D98-104. 2010
    ..Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated. DBTSS can be accessed at http://dbtss.hgc.jp/...
  14. pmc DBTSS: database of transcription start sites, progress report 2008
    Hiroyuki Wakaguri
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D97-101. 2008
    ..With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses. DBTSS is accessible at http://dbtss.hgc.jp/...
  15. pmc DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
    Yuko Makita
    Human Genome Center, The Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 32:D75-7. 2004
    ....
  16. ncbi request reprint Computational prediction of subcellular localization
    Kenta Nakai
    Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Methods Mol Biol 390:429-66. 2007
    ..In this chapter we discuss these issues and close with an example illustrating the use of the WoLF PSORT web server for localization prediction...
  17. pmc Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
    Toshiyuki Okumura
    Mitsui Knowledge Industry Co Ltd, University of Tokyo, Japan
    Nucleic Acids Res 35:W227-31. 2007
    ..thaliana) or to public motif databases (JASPAR or DBTBS) in order to find similar motifs. Melina II is a client/server system developed by using Adobe (Macromedia) Flash and is accessible over the web at http://melina.hgc.jp...
  18. ncbi request reprint Functional prediction of B. subtilis genes from their regulatory sequences
    T Yada
    Japan Science and Technology, Corporation, Tokyo, Japan
    Proc Int Conf Intell Syst Mol Biol 5:354-7. 1997
    ..Furthermore, we predicted the sigma-dependencies for each of 1415 candidate genes in the genome. Our prediction results are experimentally testable and seem useful for the post-sequencing project...
  19. ncbi request reprint [Transcriptome analyses and transcriptome databases]
    Yutaka Suzuki
    Tanpakushitsu Kakusan Koso 49:1859-65. 2004
  20. ncbi request reprint A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human
    Yosuke Hatanaka
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 20:212-21. 2008
    ..We also applied basket method analysis for seeking combinatorial activities of those conserved TFBSs...
  21. pmc DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
    Yutaka Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 30:328-31. 2002
    ....
  22. pmc DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
    Yutaka Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 32:D78-81. 2004
    ....
  23. pmc Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions
    Yutaka Suzuki
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
    Genome Res 14:1711-8. 2004
    ....
  24. ncbi request reprint An O(N2) algorithm for discovering optimal Boolean pattern pairs
    Hideo Bannai
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    IEEE/ACM Trans Comput Biol Bioinform 1:159-70. 2004
    ....
  25. ncbi request reprint Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokane dai Minato ku, Tokyo 108 8639, Japan
    Gene 350:129-36. 2005
    ....
  26. ncbi request reprint Extensive feature detection of N-terminal protein sorting signals
    Hideo Bannai
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Bioinformatics 18:298-305. 2002
    ..We adopt an approach which consists of an extensive search for simple rules and various attributes which is partially guided by human intuition...
  27. ncbi request reprint Large-scale collection and characterization of promoters of human and mouse genes
    Yutaka Suzuki
    Human Genome Center, The Institute of Medical Science, The University of Tokyo 4 6 1 Shirokanedai, Tokyo, 108 8639, Japan
    In Silico Biol 4:429-44. 2004
    ..All the data were deposited and made available through a database for comparative studies, DBTSS...
  28. pmc DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
    Nicolas Sierro
    Human Genome Center, The Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, Japan
    Nucleic Acids Res 36:D93-6. 2008
    ..DBTBS can be accessed at: http://dbtbs.hgc.jp...
  29. ncbi request reprint Review: prediction of in vivo fates of proteins in the era of genomics and proteomics
    K Nakai
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, 108-8639, Japan
    J Struct Biol 134:103-16. 2001
    ..The prediction of in vivo fates of proteins will be useful for characterizing newly identified candidate genes in a genome or for interpreting multiple spots in proteome analyses...
  30. ncbi request reprint Using simple rules on presence and positioning of motifs for promoter structure modeling and tissue-specific expression prediction
    Alexis Vandenbon
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
    Genome Inform 21:188-99. 2008
    ..We believe our model can help to increase our understanding about transcription factor cooperation and transcription initiation...
  31. pmc Intrinsic promoter activities of primary DNA sequences in the human genome
    Yuta Sakakibara
    Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    DNA Res 14:71-7. 2007
    ....
  32. pmc Modeling tissue-specific structural patterns in human and mouse promoters
    Alexis Vandenbon
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
    Nucleic Acids Res 38:17-25. 2010
    ..Together, these results illustrate the validity of our models, but also indicate that the promoter structures for some tissues are easier to model than those of others...
  33. pmc DBTGR: a database of tunicate promoters and their regulatory elements
    Nicolas Sierro
    Human Genome Center, The Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 34:D552-5. 2006
    ..At the time of writing, information about 184 promoters, containing 73 identified binding sites and >2000 newly predicted binding sites is available. This database is accessible at http://dbtgr.hgc.jp...
  34. ncbi request reprint Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data
    M J L de Hoon
    Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato ku, Tokyo, Japan
    Bioinformatics 20:i101-8. 2004
    ..We provide the corresponding RNA polymerase binding sites to enable a straightforward experimental verification of these predictions...
  35. ncbi request reprint Melina: motif extraction from promoter regions of potentially co-regulated genes
    Natalia Poluliakh
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Bioinformatics 19:423-4. 2003
    ..It is also useful to optimize the sensitivity of software with a series of different parameter settings. AVAILABILITY: Melina is available at http://www.hgc.ims.u-tokyo.ac.jp/Melina/...
  36. pmc Pseudocounts for transcription factor binding sites
    Keishin Nishida
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
    Nucleic Acids Res 37:939-44. 2009
    ..As a simple representative, we suggest the value of 0.8 for practical uses...
  37. pmc Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 36:3707-15. 2008
    ....
  38. pmc Retrotransposition as a source of new promoters
    Kohji Okamura
    Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Mol Biol Evol 25:1231-8. 2008
    ..This propensity could confer retrotransposability to promoters per se. Accordingly, the retrotransposability can explain the genesis of some alternative promoters...
  39. pmc DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 34:D86-9. 2006
    ..Third, DBTSS provides detailed sequence comparisons of user-specified TSSs. Finally, we have added TSS information for zebrafish, malaria and schyzon (a red algae model organism). DBTSS is accessible at http://dbtss.hgc.jp...
  40. ncbi request reprint Gangliosides GD1b, GT1b, and GQ1b suppress the growth of human melanoma by inhibiting interleukin-8 production: the inhibition of adenylate cyclase
    N Kanda
    Department of Dermatology, Teikyo University, School of Medicine, Tokyo, Japan
    J Invest Dermatol 117:284-93. 2001
    ..The data indicate that GD1b, GT1b, and GQ1b may suppress the growth of melanoma by inhibiting interleukin-8 production via the inhibition of adenylate cyclase...
  41. ncbi request reprint Assessment of prediction accuracy of protein function from protein--protein interaction data
    H Hishigaki
    Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo 108-8639, Japan
    Yeast 18:523-31. 2001
    ..7%, 63.6% and 52.7%, respectively. The prediction accuracy rises for proteins with more than three binding partners and thus we present the open prediction results for 16 such proteins...
  42. pmc Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction
    Alexis Vandenbon
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    DNA Res 15:3-11. 2008
    ..This model can be useful for finding promising candidate genes for wet-lab experiments and for increasing our understanding of transcriptional regulation...
  43. pmc Prediction of transcriptional terminators in Bacillus subtilis and related species
    Michiel J L de Hoon
    Human Genome Center, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo, Japan
    PLoS Comput Biol 1:e25. 2005
    ..Genome-wide predictions of Rho-independent terminators for the 57 Firmicutes are available in the Supporting Information section...
  44. ncbi request reprint Small open reading frames in 5' untranslated regions of mRnas
    Riu Yamashita
    Laboratory of Genome Database, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4 6 1, Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    C R Biol 326:987-91. 2003
    ..They require attention for further analysis to identify their biological role...
  45. ncbi request reprint An assessment of prediction algorithms for nucleosome positioning
    Yoshiaki Tanaka
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 23:169-78. 2009
    ..The oligomers commonly enriched in all five eukaryotes were only CA/TG and AC/GT. Thus, to achieve relatively high performance for a species, it is desirable to prepare the training data from the same species...
  46. pmc Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes
    Katsuki Tsuritani
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minatoku, Tokyo 108 8639, Japan
    Genome Res 17:1005-14. 2007
    ..Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution...
  47. pmc Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals
    Mitsuteru Nakao
    Human Genome Center, Institute of Medical Science, University of Tokyo Tokyo, Japan
    Nucleic Acids Res 33:2355-63. 2005
    ..Our study sheds new light on the enrichment of the human proteome through alternative splicing and related events. Our database of alternative protein isoforms is available through the internet...
  48. doi request reprint Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis
    Nicolas Sierro
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Gene 430:44-9. 2009
    ..intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently...
  49. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
    ..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org...
  50. ncbi request reprint Diverse DNA methylation statuses at alternative promoters of human genes in various tissues
    Jieun Cheong
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba, Japan
    DNA Res 13:155-67. 2006
    ..DNA methylation appears to play a significant role in differential usage of alternative promoters and may be related to functional diversification between CpG-island-containing promoters and CpG-island-less promoters...
  51. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  52. ncbi request reprint Complete sequencing and characterization of 21,243 full-length human cDNAs
    Toshio Ota
    Helix Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Nat Genet 36:40-5. 2004
    ..About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs...
  53. pmc ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
    Takeshi Obayashi
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B 14 Nagatsuta cho, Midori ku, Yokohama 226 8501, Japan
    Nucleic Acids Res 35:D863-9. 2007
    ..ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks...
  54. pmc The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
    Chisato Yamasaki
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
    Nucleic Acids Res 36:D793-9. 2008
    ....
  55. pmc PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria
    Jennifer L Gardy
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
    Nucleic Acids Res 31:3613-7. 2003
    ..This dataset, the largest of its kind, is freely available, along with the PSORT-B source code (under GNU General Public License)...
  56. pmc Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infection
    Koshiro Miura
    Department of Microbiology and Immunology, Yamaguchi University School of Medicine, 1 1 1 Minami kogushi, Ube, Yamaguchi 755 8505, Japan
    DNA Res 15:83-91. 2008
    ..It suggests that besides sigma(28), there are certain up-regulatory mechanisms at the late stage, which may be involved in the chlamydial morphological change and thus pathogenesis...
  57. doi request reprint Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells
    Izuho Hatada
    Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3 39 15 Showa Machi, Maebashi 371 8512, Japan
    J Hum Genet 53:185-91. 2008
    ..We found a genome-wide demethylation of genes. This suggests demethylation rather than methylation is important in neural differentiation...
  58. pmc Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes
    Kouichi Kimura
    Life Science Research Laboratory, Central Research Laboratory, Hitachi, Ltd, Kokubunji, Tokyo, 185 8601, Japan
    Genome Res 16:55-65. 2006
    ..Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans...
  59. pmc Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues
    Kikuya Kato
    Osaka Medical Center for Cancer and Cardiovascular Diseases, 1 3 2 Nakamichi, Higashinari ku, Osaka 537 8511, Japan
    Nucleic Acids Res 33:D533-6. 2005
    ..Data for other cancers such as lung and thyroid cancers will be added in the near future. The URL of CGED is http://cged.hgc.jp...