A flexible representation of omic knowledge for thorough analysis of microarray data

doi:10.1186/1746-4811-2-5

Plant Methods

Volume 2

Viewing options:

Abstract
Full text
PDF (1.3MB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on PubMed Central
Other articles by authors
on Google Scholar

Hasegawa Y
Seki M
Mochizuki Y
Heida N
Hirosawa K
Okamoto N
Sakurai T
Satou M
Akiyama K
Iida K
Lee K
Kanaya S
Demura T
Shinozaki K
Konagaya A
Toyoda T

on PubMed

Hasegawa Y
Seki M
Mochizuki Y
Heida N
Hirosawa K
Okamoto N
Sakurai T
Satou M
Akiyama K
Iida K
Lee K
Kanaya S
Demura T
Shinozaki K
Konagaya A
Toyoda T
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Methodology

A flexible representation of omic knowledge for thorough analysis of microarray data

Yoshikazu Hasegawa¹ , Motoaki Seki² , Yoshiki Mochizuki¹ , Naohiko Heida¹ , Katsura Hirosawa¹ , Naoki Okamoto³ , Tetsuya Sakurai⁴ , Masakazu Satou⁴ , Kenji Akiyama⁴ , Kei Iida⁵ , Kisik Lee⁶ , Shigehiko Kanaya⁷ , Taku Demura⁸ , Kazuo Shinozaki⁹ , Akihiko Konagaya¹⁰ and Tetsuro Toyoda¹

¹Phenome Informatics Team, Functional Genomics Research Group, Genomic Sciences Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan

²Plant Functional Genomics Research Team, Functional Genomics Research Group, Genomic Sciences Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan

³NEC Infomatec Systems Ltd, Sakato, Takatsu, Kawasaki, Kanagawa, Japan

⁴Integrated Genome Informatics Research Unit, Metabolomics Group, Plant Science Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan

⁵Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Tamura, Nagahama, Shiga, Japan

⁶IT technology research institute, Taehung Telcom co., Ltd., Dangsan-dong 3-ga 402, Youngdungpo-gu, Seoul, South Korea

⁷Laboratory of Comparative Genomics, Department of Bioinformatics and Genomics, Graduate School of Information Science, NARA Institute of Science and Technology, Takayama, Ikoma, Nara, Japan

⁸Morphoregulation Research Team, Plant Productivity Systems Research Group, Plant Science Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan

⁹Plant Science Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan

¹⁰Advanced Genome Information Technology Research Group, Genomic Sciences Center, RIKEN Suehiro, Tsurumi, Yokohama, Kanagawa, Japan

author email corresponding author email

Plant Methods 2006, 2:5doi:10.1186/1746-4811-2-5


Published:	2 March 2006

Additional files

Additional File 1:

Supplementary Table 1. Ranking result of significant correlations between the "functional Class" of the KEGG type metabolic pathway and clusters formed by BL-SOM of the expression profile of microarray probes under drought conditions by using GSCope3

Format: HTML Size: 509KB Download file

Additional File 2:

Supplementary Table 2. Ranking result of significant correlations between the "functional Class" of the AraCyc type metabolic pathway and the clusters formed by BL-SOM of the microarray probes of expression profile under drought conditions

Format: HTML Size: 844KB Download file

Additional File 3:

Supplementary Table 3. Ranking result of significant correlations between the "functional Class" of the Directed acyclic graphs of GO terms and the clusters formed by BL-SOM of the microarray probes of expression profile under drought conditions

Format: HTML Size: 8.5MB Download file

Additional File 4:

Supplementary Table 4. Ranking result of significant correlations between the "functional Class" of the Gene position on genome and the clusters formed by BL-SOM of the microarray probes of expression profile under drought conditions

Format: HTML Size: 5.3MB Download file

Additional File 5:

Supplementary Table 5. Ranking result of significant correlations between the "functional Class" of the "Protein-protein interaction and Arabidopsis thaliana gene expression" and the clusters formed by BL-SOM of the microarray probes of expression profile under drought conditions

Format: HTML Size: 1.1MB Download file

Additional File 6:

Supplementary Table 6. Ranking result of significant correlations between the "functional Class" of the "Comparison between gene expression of Arabidopsis thaliana and Zinia elegans" and the clusters formed by BL-SOM of the microarray probes of expression profile under drought conditions

Format: HTML Size: 90KB Download file

Additional File 7:

The relationship between the number of the first principal ingredient in the BL-SOM clusters and the index of clustering. The first principal ingredient = 3 to 20 (clustering 3 to 120) of BL-SOM clustering of the microarray data under drought stress and the index of clustering (the "mean value of each cluster's average radius" and "explained variability") is plotted. It is used for analysis because the cluster with X = 11, clustering = 33, separated enough.

Format: JPEG Size: 191KB Download file