title: Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.
abstract: The number of known mRNA transcripts in the mouse has been greatly expanded by the RIKEN Mouse Gene Encyclopedia project. Validation of their reproducible expression in a tissue is an important contribution to the study of functional genomics. In this report, we determine the expression profile of 57,931 clones on 20 mouse tissues using cDNA microarrays. Of these 57,931 clones, 22,928 clones correspond to the FANTOM2 clone set. The set represents 20,234 transcriptional units (TUs) out of 33,409 TUs in the FANTOM2 set. We identified 7206 separate clones that satisfied stringent criteria for tissue-specific expression. Gene Ontology terms were assigned for these 7206 clones, and the proportion of 'molecular function' ontology for each tissue-specific clone was examined. These data will provide insights into the function of each tissue. Tissue-specific gene expression profiles obtained using our cDNA microarrays were also compared with the data extracted from the GNF Expression Atlas based on Affymetrix microarrays. One major outcome of the RIKEN transcriptome analysis is the identification of numerous nonprotein-coding mRNAs. The expression profile was also used to obtain evidence of expression for putative noncoding RNAs. In addition, 1926 clones (70%) of 2768 clones that were categorized as "unknown EST," and 1969 (58%) clones of 3388 clones that were categorized as "unclassifiable" were also shown to be reproducibly expressed.
authors.affiliation: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Hidemasa
authors.initials: H
authors.lastname: Bono
authors.forename: Ken
authors.initials: K
authors.lastname: Yagi
authors.forename: Takeya
authors.initials: T
authors.lastname: Kasukawa
authors.forename: Itoshi
authors.initials: I
authors.lastname: Nikaido
authors.forename: Naoko
authors.initials: N
authors.lastname: Tominaga
authors.forename: Rika
authors.initials: R
authors.lastname: Miki
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Mizuno
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Tomaru
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Goto
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Nitanda
authors.forename: Daisuke
authors.initials: D
authors.lastname: Shimizu
authors.forename: Hirochika
authors.initials: H
authors.lastname: Makino
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Morita
authors.forename: Junshin
authors.initials: J
authors.lastname: Fujiyama
authors.forename: Takehito
authors.initials: T
authors.lastname: Sakai
authors.forename: Takashi
authors.initials: T
authors.lastname: Shimoji
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Okazaki
mesh_terms: D000818:Animals; D002965:Classification / Q000379:methods; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D005796:Genes / Q000235:genetics / Q000502:physiology; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009928:Organ Specificity / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D018076:DNA, Complementary