Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags

Yasunari Ogihara, Keiichi Mochida, Yasue Nemoto, Koji Murai, Yukiko Yamazaki, Tadasu Shin-I, Yuji Kohara

Research output: Contribution to journalArticle

78 Citations (Scopus)

Abstract

Compared to rice, wheat exhibits characteristic growth habits and contains complex genome constituents. To assess global changes in gene expression patterns in the wheat life cycle, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Ten wheat tissues were used to construct cDNA libraries: crown and root from 14-day-old seedlings; spikelet from early and late flowering stages; spike at the booting stage, heading date and flowering date; pistil at the heading date; and seeds at 10 and 30 days post-anthesis. Several thousand colonies were randomly selected from each of these 10 cDNA libraries and sequenced from both 5′ and 3′ ends. Consequently, a total of 116 232 sequences were accumulated and classified into 25 971 contigs based on sequence homology. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were identified. Furthermore, relationships of gene expression profiles among the 10 wheat tissues were inferred from global gene expression patterns. Genes with similar functions were grouped with one another by clustering gene expression profiles. This technique might enable estimation of the functions of anonymous genes. Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants.

Original languageEnglish
Pages (from-to)1001-1011
Number of pages11
JournalPlant Journal
Volume33
Issue number6
DOIs
Publication statusPublished - Mar 2003
Externally publishedYes

Fingerprint

Expressed Sequence Tags
Life Cycle Stages
expressed sequence tags
Triticum
Cluster Analysis
life cycle (organisms)
Gene Expression
gene expression
wheat
flowering
heading
Gene Library
Transcriptome
cDNA libraries
inflorescences
genes
pistil
growth habit
Sequence Homology
Genomics

Keywords

  • Correlation clustering of expression patterns
  • Functional genomics
  • Gene search in wheat
  • Hexaploid wheat
  • Large-scale EST analysis
  • Virtual display

ASJC Scopus subject areas

  • Plant Science

Cite this

Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. / Ogihara, Yasunari; Mochida, Keiichi; Nemoto, Yasue; Murai, Koji; Yamazaki, Yukiko; Shin-I, Tadasu; Kohara, Yuji.

In: Plant Journal, Vol. 33, No. 6, 03.2003, p. 1001-1011.

Research output: Contribution to journalArticle

Ogihara, Yasunari ; Mochida, Keiichi ; Nemoto, Yasue ; Murai, Koji ; Yamazaki, Yukiko ; Shin-I, Tadasu ; Kohara, Yuji. / Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. In: Plant Journal. 2003 ; Vol. 33, No. 6. pp. 1001-1011.
@article{c5f1b3d4c9fe4afe8f658f2f2e4a772e,
title = "Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags",
abstract = "Compared to rice, wheat exhibits characteristic growth habits and contains complex genome constituents. To assess global changes in gene expression patterns in the wheat life cycle, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Ten wheat tissues were used to construct cDNA libraries: crown and root from 14-day-old seedlings; spikelet from early and late flowering stages; spike at the booting stage, heading date and flowering date; pistil at the heading date; and seeds at 10 and 30 days post-anthesis. Several thousand colonies were randomly selected from each of these 10 cDNA libraries and sequenced from both 5′ and 3′ ends. Consequently, a total of 116 232 sequences were accumulated and classified into 25 971 contigs based on sequence homology. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were identified. Furthermore, relationships of gene expression profiles among the 10 wheat tissues were inferred from global gene expression patterns. Genes with similar functions were grouped with one another by clustering gene expression profiles. This technique might enable estimation of the functions of anonymous genes. Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants.",
keywords = "Correlation clustering of expression patterns, Functional genomics, Gene search in wheat, Hexaploid wheat, Large-scale EST analysis, Virtual display",
author = "Yasunari Ogihara and Keiichi Mochida and Yasue Nemoto and Koji Murai and Yukiko Yamazaki and Tadasu Shin-I and Yuji Kohara",
year = "2003",
month = "3",
doi = "10.1046/j.1365-313X.2003.01687.x",
language = "English",
volume = "33",
pages = "1001--1011",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "6",

}

TY - JOUR

T1 - Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags

AU - Ogihara, Yasunari

AU - Mochida, Keiichi

AU - Nemoto, Yasue

AU - Murai, Koji

AU - Yamazaki, Yukiko

AU - Shin-I, Tadasu

AU - Kohara, Yuji

PY - 2003/3

Y1 - 2003/3

N2 - Compared to rice, wheat exhibits characteristic growth habits and contains complex genome constituents. To assess global changes in gene expression patterns in the wheat life cycle, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Ten wheat tissues were used to construct cDNA libraries: crown and root from 14-day-old seedlings; spikelet from early and late flowering stages; spike at the booting stage, heading date and flowering date; pistil at the heading date; and seeds at 10 and 30 days post-anthesis. Several thousand colonies were randomly selected from each of these 10 cDNA libraries and sequenced from both 5′ and 3′ ends. Consequently, a total of 116 232 sequences were accumulated and classified into 25 971 contigs based on sequence homology. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were identified. Furthermore, relationships of gene expression profiles among the 10 wheat tissues were inferred from global gene expression patterns. Genes with similar functions were grouped with one another by clustering gene expression profiles. This technique might enable estimation of the functions of anonymous genes. Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants.

AB - Compared to rice, wheat exhibits characteristic growth habits and contains complex genome constituents. To assess global changes in gene expression patterns in the wheat life cycle, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Ten wheat tissues were used to construct cDNA libraries: crown and root from 14-day-old seedlings; spikelet from early and late flowering stages; spike at the booting stage, heading date and flowering date; pistil at the heading date; and seeds at 10 and 30 days post-anthesis. Several thousand colonies were randomly selected from each of these 10 cDNA libraries and sequenced from both 5′ and 3′ ends. Consequently, a total of 116 232 sequences were accumulated and classified into 25 971 contigs based on sequence homology. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were identified. Furthermore, relationships of gene expression profiles among the 10 wheat tissues were inferred from global gene expression patterns. Genes with similar functions were grouped with one another by clustering gene expression profiles. This technique might enable estimation of the functions of anonymous genes. Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants.

KW - Correlation clustering of expression patterns

KW - Functional genomics

KW - Gene search in wheat

KW - Hexaploid wheat

KW - Large-scale EST analysis

KW - Virtual display

UR - http://www.scopus.com/inward/record.url?scp=0037356771&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0037356771&partnerID=8YFLogxK

U2 - 10.1046/j.1365-313X.2003.01687.x

DO - 10.1046/j.1365-313X.2003.01687.x

M3 - Article

C2 - 12631325

AN - SCOPUS:0037356771

VL - 33

SP - 1001

EP - 1011

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

IS - 6

ER -