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Literature DB >> 14681478

EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.

Itoshi Nikaido¹, Chika Saito, Akiko Wakamoto, Yasuhiro Tomaru, Takahiro Arakawa, Yoshihide Hayashizaki, Yasushi Okazaki.

Abstract

We have developed an integrated database that is specialized for the study of imprinted disease genes. The database contains novel candidate imprinted genes identified by the RIKEN full-length mouse cDNA microarray study, information on validated single nucleotide polymorphisms (SNPs) to confirm imprinting using reciprocal mouse crosses and the predicted physical position of imprinting-related disease loci in the mouse and human genomes. It has two user-friendly search interfaces: the SNP-central view (MuSCAT: MoUse SNP CATalog) and the candidate gene-central view (CITE: Candidate Imprinted Transcripts by Expression). The database, EICO (Expression-based Imprint Candidate Organizer), can be accessed via the World Wide Web (http://fantom2.gsc.riken.jp/EICODB/) and the DAS client software. These data and interfaces facilitate understanding of the mechanism of imprinting in mammalian inherited traits.

Entities: Species

Mesh：

Substances：
DNA, Complementary

Year: 2004 PMID： 14681478 PMCID： PMC308827 DOI： 10.1093/nar/gkh093

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

16 in total

1. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Authors: Y Okazaki; M Furuno; T Kasukawa; J Adachi; H Bono; S Kondo; I Nikaido; N Osato; R Saito; H Suzuki; I Yamanaka; H Kiyosawa; K Yagi; Y Tomaru; Y Hasegawa; A Nogami; C Schönbach; T Gojobori; R Baldarelli; D P Hill; C Bult; D A Hume; J Quackenbush; L M Schriml; A Kanapin; H Matsuda; S Batalov; K W Beisel; J A Blake; D Bradt; V Brusic; C Chothia; L E Corbani; S Cousins; E Dalla; T A Dragani; C F Fletcher; A Forrest; K S Frazer; T Gaasterland; M Gariboldi; C Gissi; A Godzik; J Gough; S Grimmond; S Gustincich; N Hirokawa; I J Jackson; E D Jarvis; A Kanai; H Kawaji; Y Kawasawa; R M Kedzierski; B L King; A Konagaya; I V Kurochkin; Y Lee; B Lenhard; P A Lyons; D R Maglott; L Maltais; L Marchionni; L McKenzie; H Miki; T Nagashima; K Numata; T Okido; W J Pavan; G Pertea; G Pesole; N Petrovsky; R Pillai; J U Pontius; D Qi; S Ramachandran; T Ravasi; J C Reed; D J Reed; J Reid; B Z Ring; M Ringwald; A Sandelin; C Schneider; C A M Semple; M Setou; K Shimada; R Sultana; Y Takenaka; M S Taylor; R D Teasdale; M Tomita; R Verardo; L Wagner; C Wahlestedt; Y Wang; Y Watanabe; C Wells; L G Wilming; A Wynshaw-Boris; M Yanagisawa; I Yang; L Yang; Z Yuan; M Zavolan; Y Zhu; A Zimmer; P Carninci; N Hayatsu; T Hirozane-Kishikawa; H Konno; M Nakamura; N Sakazume; K Sato; T Shiraki; K Waki; J Kawai; K Aizawa; T Arakawa; S Fukuda; A Hara; W Hashizume; K Imotani; Y Ishii; M Itoh; I Kagawa; A Miyazaki; K Sakai; D Sasaki; K Shibata; A Shinagawa; A Yasunishi; M Yoshino; R Waterston; E S Lander; J Rogers; E Birney; Y Hayashizaki
Journal: Nature Date: 2002-12-05 Impact factor: 49.962

2. Ensembl 2002: accommodating comparative genomics.

Authors: M Clamp; D Andrews; D Barker; P Bevan; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; T Hubbard; A Kasprzyk; D Keefe; H Lehvaslaiho; V Iyer; C Melsopp; E Mongin; R Pettett; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; E Birney
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

3. 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

4. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

Authors: Ada Hamosh; Alan F Scott; Joanna Amberger; Carol Bocchini; David Valle; Victor A McKusick
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

5. Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

Authors: B Ewing; L Hillier; M C Wendl; P Green
Journal: Genome Res Date: 1998-03 Impact factor: 9.043

6. Base-calling of automated sequencer traces using phred. II. Error probabilities.

Authors: B Ewing; P Green
Journal: Genome Res Date: 1998-03 Impact factor: 9.043

Review 7. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors: S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal: Nucleic Acids Res Date: 1997-09-01 Impact factor: 16.971

8. Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray.

Authors: Yosuke Mizuno; Yusuke Sotomaru; Yukiko Katsuzawa; Tomohiro Kono; Makiko Meguro; Mitsuo Oshimura; Jun Kawai; Yasuhiro Tomaru; Hidenori Kiyosawa; Itoshi Nikaido; Hiroshi Amanuma; Yoshihide Hayashizaki; Yasushi Okazaki
Journal: Biochem Biophys Res Commun Date: 2002-02-08 Impact factor: 3.575

9. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.

Authors: Koji Numata; Akio Kanai; Rintaro Saito; Shinji Kondo; Jun Adachi; Laurens G Wilming; David A Hume; Yoshihide Hayashizaki; Masaru Tomita
Journal: Genome Res Date: 2003-06 Impact factor: 9.043

10. The distributed annotation system.

Authors: R D Dowell; R M Jokerst; A Day; S R Eddy; L Stein
Journal: BMC Bioinformatics Date: 2001-10-10 Impact factor: 3.169

6 in total

1. The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide.

Authors: Rituparna Mukhopadhyay; WenQiang Yu; Joanne Whitehead; JunWang Xu; Magda Lezcano; Svetlana Pack; Chandrasekhar Kanduri; Meena Kanduri; Vasudeva Ginjala; Alexander Vostrov; Wolfgang Quitschke; Igor Chernukhin; Elena Klenova; Victor Lobanenkov; Rolf Ohlsson
Journal: Genome Res Date: 2004-07-15 Impact factor: 9.043

2. Investigation of a patient with a partial trisomy 16q including the fat mass and obesity associated gene (FTO): fine mapping and FTO gene expression study.

Authors: Linda van den Berg; Henriette Delemarre-van de Waal; Joan C Han; Bauke Ylstra; Paul Eijk; Maria Nesterova; Peter Heutink; Constantine A Stratakis
Journal: Am J Med Genet A Date: 2010-03 Impact factor: 2.802

3. Real-time PCR analysis of candidate imprinted genes on mouse chromosome 11 shows balanced expression from the maternal and paternal chromosomes and strain-specific variation in expression levels.

Authors: Robert G Tuskan; Shirley Tsang; Zhonghe Sun; Jessica Baer; Ester Rozenblum; Xiaolin Wu; David J Munroe; Karlyne M Reilly
Journal: Epigenetics Date: 2007-12-20 Impact factor: 4.528