Literature DB >> 11752296

READ: RIKEN Expression Array Database.

Hidemasa Bono1, Takeya Kasukawa, Yoshihide Hayashizaki, Yasushi Okazaki.   

Abstract

READ, the RIKEN Expression Array Database, is a database of expression profile data from the RIKEN mouse cDNA microarray. It stores the microarray experimental data and information, and provides Web interfaces for researchers to use to retrieve, analyze and display their data. The goals for READ are to serve as a storage site for microarray data from ongoing research in the RIKEN mouse encyclopedia project and to provide useful links and tools to decipher biologically important information. The gene information is based mainly on the fully annotated FANTOM database. READ can be accessed at http://read.gsc.riken.go.jp/. READ also provides a search tool [READ integrates gene expression neighbor (RINGENE)] for genes with similarities in expression profiling.

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Year:  2002        PMID: 11752296      PMCID: PMC99103          DOI: 10.1093/nar/30.1.211

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  6 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.

Authors:  R Miki; K Kadota; H Bono; Y Mizuno; Y Tomaru; P Carninci; M Itoh; K Shibata; J Kawai; H Konno; S Watanabe; K Sato; Y Tokusumi; N Kikuchi; Y Ishii; Y Hamaguchi; I Nishizuka; H Goto; H Nitanda; S Satomi; A Yoshiki; M Kusakabe; J L DeRisi; M B Eisen; V R Iyer; P O Brown; M Muramatsu; H Shimada; Y Okazaki; Y Hayashizaki
Journal:  Proc Natl Acad Sci U S A       Date:  2001-02-27       Impact factor: 11.205

3.  Viva la revolution! A report from the FANTOM meeting.

Authors:  J Quackenbush
Journal:  Nat Genet       Date:  2000-11       Impact factor: 38.330

4.  Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data.

Authors:  K Kadota; R Miki; H Bono; K Shimizu; Y Okazaki; Y Hayashizaki
Journal:  Physiol Genomics       Date:  2001-01-19       Impact factor: 3.107

5.  Functional annotation of a full-length mouse cDNA collection.

Authors:  J Kawai; A Shinagawa; K Shibata; M Yoshino; M Itoh; Y Ishii; T Arakawa; A Hara; Y Fukunishi; H Konno; J Adachi; S Fukuda; K Aizawa; M Izawa; K Nishi; H Kiyosawa; S Kondo; I Yamanaka; T Saito; Y Okazaki; T Gojobori; H Bono; T Kasukawa; R Saito; K Kadota; H Matsuda; M Ashburner; S Batalov; T Casavant; W Fleischmann; T Gaasterland; C Gissi; B King; H Kochiwa; P Kuehl; S Lewis; Y Matsuo; I Nikaido; G Pesole; J Quackenbush; L M Schriml; F Staubli; R Suzuki; M Tomita; L Wagner; T Washio; K Sakai; T Okido; M Furuno; H Aono; R Baldarelli; G Barsh; J Blake; D Boffelli; N Bojunga; P Carninci; M F de Bonaldo; M J Brownstein; C Bult; C Fletcher; M Fujita; M Gariboldi; S Gustincich; D Hill; M Hofmann; D A Hume; M Kamiya; N H Lee; P Lyons; L Marchionni; J Mashima; J Mazzarelli; P Mombaerts; P Nordone; B Ring; M Ringwald; I Rodriguez; N Sakamoto; H Sasaki; K Sato; C Schönbach; T Seya; Y Shibata; K F Storch; H Suzuki; K Toyo-oka; K H Wang; C Weitz; C Whittaker; L Wilming; A Wynshaw-Boris; K Yoshida; Y Hasegawa; H Kawaji; S Kohtsuki; Y Hayashizaki
Journal:  Nature       Date:  2001-02-08       Impact factor: 49.962

6.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

  6 in total
  14 in total

1.  Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Authors:  Takeya Kasukawa; Masaaki Furuno; Itoshi Nikaido; Hidemasa Bono; David A Hume; Carol Bult; David P Hill; Richard Baldarelli; Julian Gough; Alexander Kanapin; Hideo Matsuda; Lynn M Schriml; Yoshihide Hayashizaki; Yasushi Okazaki; John Quackenbush
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

2.  The mouse secretome: functional classification of the proteins secreted into the extracellular environment.

Authors:  Sean M Grimmond; Kevin C Miranda; Zheng Yuan; Melissa J Davis; David A Hume; Ken Yagi; Naoko Tominaga; Hidemasa Bono; Yoshihide Hayashizaki; Yasushi Okazaki; Rohan D Teasdale
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

3.  Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome.

Authors:  Timothy Ravasi; Thomas Huber; Mihaela Zavolan; Alistair Forrest; Terry Gaasterland; Sean Grimmond; David A Hume
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

4.  MiR-508-3p promotes proliferation and inhibits apoptosis of middle ear cholesteatoma cells by targeting PTEN/PI3K/AKT pathway.

Authors:  Dongliang Liu; Xiulan Ma
Journal:  Int J Med Sci       Date:  2021-07-11       Impact factor: 3.738

5.  Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.

Authors:  Hidemasa Bono; Ken Yagi; Takeya Kasukawa; Itoshi Nikaido; Naoko Tominaga; Rika Miki; Yosuke Mizuno; Yasuhiro Tomaru; Hitoshi Goto; Hiroyuki Nitanda; Daisuke Shimizu; Hirochika Makino; Tomoyuki Morita; Junshin Fujiyama; Takehito Sakai; Takashi Shimoji; David A Hume; Yoshihide Hayashizaki; Yasushi Okazaki
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

6.  Comprehensive analysis of the mouse metabolome based on the transcriptome.

Authors:  Hidemasa Bono; Itoshi Nikaido; Takeya Kasukawa; Yoshihide Hayashizaki; Yasushi Okazaki
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

Review 7.  Databases of free expression.

Authors:  John R Walker; Tim Wiltshire
Journal:  Mamm Genome       Date:  2006-12-01       Impact factor: 3.224

8.  The RIKEN integrated database of mammals.

Authors:  Hiroshi Masuya; Yuko Makita; Norio Kobayashi; Koro Nishikata; Yuko Yoshida; Yoshiki Mochizuki; Koji Doi; Terue Takatsuki; Kazunori Waki; Nobuhiko Tanaka; Manabu Ishii; Akihiro Matsushima; Satoshi Takahashi; Atsushi Hijikata; Kouji Kozaki; Teiichi Furuichi; Hideya Kawaji; Shigeharu Wakana; Yukio Nakamura; Atsushi Yoshiki; Takehide Murata; Kaoru Fukami-Kobayashi; Sujatha Mohan; Osamu Ohara; Yoshihide Hayashizaki; Riichiro Mizoguchi; Yuichi Obata; Tetsuro Toyoda
Journal:  Nucleic Acids Res       Date:  2010-11-13       Impact factor: 16.971

9.  Modulated contact frequencies at gene-rich loci support a statistical helix model for mammalian chromatin organization.

Authors:  Franck Court; Julie Miro; Caroline Braem; Marie-Noëlle Lelay-Taha; Audrey Brisebarre; Florian Atger; Thierry Gostan; Michaël Weber; Guy Cathala; Thierry Forné
Journal:  Genome Biol       Date:  2011-05-10       Impact factor: 13.583

10.  Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

Authors:  Diego G Silva; Christian Schönbach; Vladimir Brusic; Luis A Socha; Takeshi Nagashima; Nikolai Petrovsky
Journal:  BMC Genomics       Date:  2004-04-29       Impact factor: 3.969

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