Skip Navigation

Nucleic Acids Research 2005 33(Web Server Issue):W753-W757; doi:10.1093/nar/gki451
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1527K) Freely available
Right arrow Screen PDF (358K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Saito, T. L.
Right arrow Articles by Morishita, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Saito, T. L.
Right arrow Articles by Morishita, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Data mining tools for the Saccharomyces cerevisiae morphological database

Taro L. Saito1,4, Jun Sese2, Yoichiro Nakatani2,4, Fumi Sano3,4, Masashi Yukawa3,4, Yoshikazu Ohya3,4 and Shinichi Morishita2,4,*

1Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 2Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo Building FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan 3Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo Building FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan 4Japan and Institute for Bioinformatics and Research and Development, Japan Science and Technology Corporation Science Plaza, 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666, Japan

*To whom correspondence should be addressed. Tel: +81 4 7136 3985; Fax: +81 4 7136 3977; Email: moris{at}k.u-tokyo.ac.jp

Received February 14, 2005. Revised March 31, 2005. Accepted March 31, 2005.

For comprehensive understanding of precise morphological changes resulting from loss-of-function mutagenesis, a large collection of 1 899 247 cell images was assembled from 91 271 micrographs of 4782 budding yeast disruptants of non-lethal genes. All the cell images were processed computationally to measure ~500 morphological parameters in individual mutants. We have recently made this morphological quantitative data available to the public through the Saccharomyces cerevisiae Morphological Database (SCMD). Inspecting the significance of morphological discrepancies between the wild type and the mutants is expected to provide clues to uncover genes that are relevant to the biological processes producing a particular morphology. To facilitate such intensive data mining, a suite of new software tools for visualizing parameter value distributions was developed to present mutants with significant changes in easily understandable forms. In addition, for a given group of mutants associated with a particular function, the system automatically identifies a combination of multiple morphological parameters that discriminates a mutant group from others significantly, thereby characterizing the function effectively. These data mining functions are available through the World Wide Web at http://scmd.gi.k.u-tokyo.ac.jp/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 RNAHome page
H. Yamada, C. Horigome, T. Okada, C. Shirai, and K. Mizuta
Yeast Rrp14p is a nucleolar protein involved in both ribosome biogenesis and cell polarity
RNA, November 1, 2007; 13(11): 1977 - 1987.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
R. Sopko and B. Andrews
Small open reading frames: Not so small anymore.
Genome Res., March 1, 2006; 16(3): 314 - 315.
[Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Y. Ohya, J. Sese, M. Yukawa, F. Sano, Y. Nakatani, T. L. Saito, A. Saka, T. Fukuda, S. Ishihara, S. Oka, et al.
High-dimensional and large-scale phenotyping of yeast mutants
PNAS, December 27, 2005; 102(52): 19015 - 19020.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.