title: Global gene expression profiling and cluster analysis in Xenopus laevis.
abstract: We have undertaken a large-scale microarray gene expression analysis using cDNAs corresponding to 21,000 Xenopus laevis ESTs. mRNAs from 37 samples, including embryos and adult organs, were profiled. Cluster analysis of embryos of different stages was carried out and revealed expected affinities between gastrulae and neurulae, as well as between advanced neurulae and tadpoles, while egg and feeding larvae were clearly separated. Cluster analysis of adult organs showed some unexpected tissue-relatedness, e.g. kidney is more related to endodermal than to mesodermal tissues and the brain is separated from other neuroectodermal derivatives. Cluster analysis of genes revealed major phases of co-ordinate gene expression between egg and adult stages. During the maternal-early embryonic phase, genes maintaining a rapidly dividing cell state are predominantly expressed (cell cycle regulators, chromatin proteins). Genes involved in protein biosynthesis are progressively induced from mid-embryogenesis onwards. The larval-adult phase is characterised by expression of genes involved in metabolism and terminal differentiation. Thirteen potential synexpression groups were identified, which encompass components of diverse molecular processes or supra-molecular structures, including chromatin, RNA processing and nucleolar function, cell cycle, respiratory chain/Krebs cycle, protein biosynthesis, endoplasmic reticulum, vesicle transport, synaptic vesicle, microtubule, intermediate filament, epithelial proteins and collagen. Data filtering identified genes with potential stage-, region- and organ-specific expression. The dataset was assembled in the iChip microarray database, , which allows user-defined queries. The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes.
authors.affiliation: Division of Molecular Embryology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: Danila
authors.initials: D
authors.lastname: Baldessari
authors.forename: Yongchol
authors.initials: Y
authors.lastname: Shin
authors.forename: Olga
authors.initials: O
authors.lastname: Krebs
authors.forename: Rainer
authors.initials: R
authors.lastname: König
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Koide
authors.forename: Arunachalam
authors.initials: A
authors.lastname: Vinayagam
authors.forename: Ursula
authors.initials: U
authors.lastname: Fenger
authors.forename: Makoto
authors.initials: M
authors.lastname: Mochii
authors.forename: Chie
authors.initials: C
authors.lastname: Terasaka
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kitayama
authors.forename: Daniel
authors.initials: D
authors.lastname: Peiffer
authors.forename: Naoto
authors.initials: N
authors.lastname: Ueno
authors.forename: Roland
authors.initials: R
authors.lastname: Eils
authors.forename: Ken W
authors.initials: KW
authors.lastname: Cho
authors.forename: Christof
authors.initials: C
authors.lastname: Niehrs
mesh_terms: D000818:Animals; D003001:Cloning, Molecular; D016000:Cluster Analysis; D003094:Collagen / Q000378:metabolism; D018076:DNA, Complementary / Q000378:metabolism; D030541:Databases, Genetic; D030562:Databases, Protein; D047108:Embryonic Development; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000378:metabolism; D013997:Time Factors; D014018:Tissue Distribution; D014981:Xenopus; D014982:Xenopus laevis / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012313:RNA; D003094:Collagen