Yukihisa Shimada talks with
ScienceWatch.com and answers a few questions about
this month's New Hot Paper in the field of Plant & Animal
Article Title: The AtGenExpress hormone and chemical
treatment data set: experimental design, data evaluation, model
data analysis and data access
Authors: Goda, H., et al.
Journal: PLANT J, Volume: 55, Issue: 3, Page:
526-542, Year: AUG 2008
* RIKEN, Plant Sci Ctr, Kanagawa 2300045, Japan.
* RIKEN, Plant Sci Ctr, Kanagawa 2300045, Japan.
* Nagoya Univ, Sch Agr, Mol Microbiol Lab, Chikusa Ku,
Nagoya, Aichi 4648601, Japan.
(addresses have been
Why do you think your paper is highly
As part of an international research effort, the AtGenExpress consortium
was organized to make an important contribution to the scientific community
by the accumulation of large-scale transcriptome datasets. This data has
been available without charge for public access since 2004.
Together with the other contributions of the AtGenExpress project, our
dataset composes a large-scale transcriptome database. This data
constitutes one of the earliest infrastructures made freely available for
public access for conducting systems biology in multicellular organisms
across a very large scale.
Does it describe a new discovery, methodology, or
synthesis of knowledge?
One purpose of this study was to establish a comprehensive database in
order to facilitate gene-expression pattern searches. However, another and
more ambitious motivation was to analyze genome-wide co-expression in
Arabidopsis, so that
the functions of unknown genes can be predicted based on similarities
between their expression patterns and those of known genes.
"Our data and model studies will be useful in many of
the aspects of biological studies, such as gene hunting,
systems biology, and hormone studies"
Until quite recently, in the eukaryotes, the only and most reliable
approach to predict the functions of unknown genes was to conduct an
analysis of the amino acid sequence of the encoded protein, such as
homology analysis or motif analysis of the amino acid sequence.
On the one hand, in the prokaryote genome, functionally related genes form
an operon structure, in order to maintain coordinated expression of the
genes in the operon. Since the genes included in the identical operon
participate in the same biological functions, operon structure is an
important clue used to identify the gene's function, especially when there
is no clue from the amino acid sequence alone.
In general, since no general rule has been yet found between a gene's
function and their chromosomal positions in the eukaryotes, it is
impossible to predict a gene's function from the positional relation of the
gene in the genome.
Would you summarize the significance of your paper
in layman's terms?
We analyzed global gene expression in Arabidopsis in response to
various hormones—auxin, cytokinin, gibberellin, brassinosteroid,
abscisic acid, jasmonate, and ethylene—and in related experiments as
part of the AtGenExpress project. This was reported for the first time in
plants. Hormone-inducible genes were identified from the hormone-response
We also analyzed relationships among the expression profiles of hormone
response and those included in the AtGenExpress stress response, using a
correlation coefficient. This approach was useful in monitoring the
hormonal status of stress-related samples.
Genome-wide transcriptional gene-to-gene correlations were also analyzed,
and the result indicated that our dataset is useful when used to find
clusters of co-expressed genes, and also to predict the functions of
unknown genes. The dataset presented here will be a versatile resource for
future hormone studies and constitutes a reference of genome-wide gene
expression in Arabidopsis.
How did you become involved in this research, and
were there any problems along the way?
I began my transcriptome studies of plant hormone actions at RIKEN. This
work has been supported by a RIKEN Plant Science Center (PSC) project. Many
collaborators have also supported this project, and their contributions
were of great value. I would therefore like to take a moment to express my
profound appreciation for their efforts.
Where do you see your research leading in the
Our data and model studies will be useful in many of the aspects of
biological studies, such as gene hunting, systems biology, and hormone
Do you foresee any social or political
implications for your research?
We are currently developing a system to help us to discover a drug that
regulates hormone actions based primarily on our genomics data. This study
may assist in the development of a novel agricultural technology.
Yukihisa Shimada, Ph.D.
Integrated Genomics Research Team Unit leader
RIKEN Yokohama Institute
Plant Science Center
Yokohama City, Kanagawa, Japan
KEYWORDS: CHEMICAL GENOMICS; PHYTOHORMONE NETWORK ANALYSIS; CO-EXPRESSION
NETWORK ANALYSIS; SYSTEMS BIOLOGY; ATGENEXPRESS; BRASSINOSTEROID-REGULATED
GENES; ARABIDOPSIS RESPONSE REGULATOR; MICROARRAY DATA; GIBBERELLIN
BIOSYNTHESIS; COEXPRESSION NETWORKS; TRANSCRIPTION FACTOR; EXPRESSION
ANALYSIS; SEED-GERMINATION; THALIANA; CYTOCHROME-P450.