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

被引：18

作者：

Nikaido, I

Saito, C

Wakamoto, A

Tomaru, Y

Arakawa, T

Hayashizaki, Y

Okazaki, Y

机构：

[1] Saitama Med Sch, Div Funct Genom & Syst Med, Res Ctr Genom Med, Hidaka, Saitama 3501241, Japan

[2] Yokohama City Univ, Div Genom Informat Resource Explorat, Grad Sch Integrated Sci, Kanagawa 2300045, Japan

[3] RIKEN Yokohama Inst, RIKEN Genom Sci Ctr, Lab Genome Explorat Res Grp, Kanagawa 2300045, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2004年 / 32卷

关键词：

D O I：

10.1093/nar/gkh093

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D548 / D551

页数：4

共 16 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] FANTOM DB: Database of functional annotation of RIKEN mouse cDNA clones [J].

Bono, H ;

Kasukawa, T ;

Furuno, M ;

Hayashizaki, Y ;

Okazaki, Y .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :116-118

[3] Ensembl 2002: accommodating comparative genomics [J].

Clamp, M ;

Andrews, D ;

Barker, D ;

Bevan, P ;

Cameron, G ;

Chen, Y ;

Clark, L ;

Cox, T ;

Cuff, J ;

Curwen, V ;

Down, T ;

Durbin, R ;

Eyras, E ;

Gilbert, J ;

Hammond, M ;

Hubbard, T ;

Kasprzyk, A ;

Keefe, D ;

Lehvaslaiho, H ;

Iyer, V ;

Melsopp, C ;

Mongin, E ;

Pettett, R ;

Potter, S ;

Rust, A ;

Schmidt, E ;

Searle, S ;

Slater, G ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Stupka, E ;

Ureta-Vidal, A ;

Vastrik, I ;

Birney, E .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :38-42

[4] The Distributed Annotation System [J].

Dowell, Robin D. ;

Jokerst, Rodney M. ;

Day, Allen ;

Eddy, Sean R. ;

Stein, Lincoln .

BMC BIOINFORMATICS, 2001, 2 (1)

[5] Base-calling of automated sequencer traces using phred.: II.: Error probabilities [J].

Ewing, B ;

Green, P .

GENOME RESEARCH, 1998, 8 (03) :186-194

[6] Base-calling of automated sequencer traces using phred.: I.: Accuracy assessment [J].

Ewing, B ;

Hillier, L ;

Wendl, MC ;

Green, P .

GENOME RESEARCH, 1998, 8 (03) :175-185

[7] Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders [J].

Hamosh, A ;

Scott, AF ;

Amberger, J ;

Bocchini, C ;

Valle, D ;

McKusick, VA .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :52-55

[8] Development and evaluation of an automated annotation pipeline and cDNA annotation system [J].

Kasukawa, T ;

Furuno, M ;

Nikaido, I ;

Bono, H ;

Hume, DA ;

Bult, C ;

Hill, DP ;

Baldarelli, R ;

Gough, J ;

Kanapin, A ;

Matsuda, H ;

Schriml, LM ;

Hayashizaki, Y ;

Okazaki, Y ;

Quackenbush, J .

GENOME RESEARCH, 2003, 13 (6B) :1542-1551

[9] Antisense transcripts with FANTOM2 clone set and their implications for gene regulation [J].

Kiyosawa, H ;

Yamanaka, I ;

Osato, N ;

Kondo, S ;

Hayashizaki, Y .

GENOME RESEARCH, 2003, 13 (6B) :1324-1334

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

Mizuno, Y ;

Sotomaru, Y ;

Katsuzawa, Y ;

Kono, T ;

Meguro, M ;

Oshimura, M ;

Kawai, J ;

Tomaru, Y ;

Kiyosawa, H ;

Nikaido, I ;

Amanuma, H ;

Hayashizaki, Y ;

Okazaki, Y .

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2002, 290 (05) :1499-1505

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