title: Gene expression profile during the life cycle of the urochordate Ciona intestinalis.
abstract: 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.
authors.affiliation: Division of Innovative Research, Creative Research Initiative Sousei, Hokkaido University, N21W10 Kita-ku, Sapporo 001-0021, Japan. azumi@cris.hokudai.ac.jp
authors.forename: Kaoru
authors.initials: K
authors.lastname: Azumi
authors.forename: Sorin V
authors.initials: SV
authors.lastname: Sabau
authors.forename: Manabu
authors.initials: M
authors.lastname: Fujie
authors.forename: Takeshi
authors.initials: T
authors.lastname: Usami
authors.forename: Ryo
authors.initials: R
authors.lastname: Koyanagi
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawashima
authors.forename: Shigeki
authors.initials: S
authors.lastname: Fujiwara
authors.forename: Michio
authors.initials: M
authors.lastname: Ogasawara
authors.forename: Masanobu
authors.initials: M
authors.lastname: Satake
authors.forename: Masaru
authors.initials: M
authors.lastname: Nonaka
authors.forename: Hong-Gang
authors.initials: HG
authors.lastname: Wang
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Satou
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
mesh_terms: 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