Gene expression profile during the life cycle of the urochordate Ciona intestinalis.
Recent whole-genome studies and in-depth expressed sequence tag (EST) analyses have identified most of the developmentally relevant genes in the urochordate, Ciona intestinalis. In this study, we made use of a large-scale oligo-DNA microarray to further investigate and identify genes with specific or correlated expression profiles, and we report global gene expression profiles for about 66% of all the C. intestinalis genes that are expressed during its life cycle. We succeeded in categorizing the data set into 5 large clusters and 49 sub-clusters based on the expression profile of each gene. This revealed the higher order of gene expression profiles during the developmental and aging stages. Furthermore, a combined analysis of microarray data with the EST database revealed the gene groups that were expressed at a specific stage or in a specific organ of the adult. This study provides insights into the complex structure of ascidian gene expression, identifies co-expressed gene groups and marker genes and makes predictions for the biological roles of many uncharacterized genes. This large-scale oligo-DNA microarray for C. intestinalis should facilitate the understanding of global gene expression and gene networks during the development and aging of a basal chordate.
Azumi
Kaoru
K
Division of Innovative Research, Creative Research Initiative Sousei, Hokkaido University, N21W10 Kita-ku, Sapporo 001-0021, Japan. azumi@cris.hokudai.ac.jp
Sabau
Sorin V
SV
Fujie
Manabu
M
Usami
Takeshi
T
Koyanagi
Ryo
R
Kawashima
Takeshi
T
Fujiwara
Shigeki
S
Ogasawara
Michio
M
Satake
Masanobu
M
Nonaka
Masaru
M
Wang
Hong-Gang
HG
Satou
Yutaka
Y
Satoh
Nori
N
D000818:Animals; D002938:Ciona intestinalis / Q000196:embryology / Q000235:genetics* / Q000254:growth & development* / Q000276:immunology; D005260:Female; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D018507:Gene Expression Regulation, Developmental; D007109:Immunity / Q000235:genetics; D008297:Male; D005810:Multigene Family; D009672:Notochord / Q000196:embryology / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D009928:Organ Specificity; D015203:Reproducibility of Results