A genome-wide and nonredundant mouse transcription factor database

被引：104

作者：

Kanamori, M

Konno, H

Osato, N

Kawai, J

Hayashizaki, Y

Suzuki, H

机构：

[1] RIKEN, GSC, Lab Genome Explorat Res Grp, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[2] RIKEN, Genome Sci Lab, Wako, Saitama 3510198, Japan

来源：

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS | 2004年 / 322卷 / 03期

关键词：

mouse; transcription factor; database; gene ontology; LocusLink; annotation; cDNA clones;

D O I：

10.1016/j.bbrc.2004.07.179

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：

Here we describe the development of a genome-wide and nonredundant mouse transcription factor database and its viewer (http://genome.gsc.riken.jp/TFdb/). We systematically selected transcription factors with DNA-binding properties and their regulators on the basis of their LocusLink and Gene Ontology annotations. We also incorporated into our database information regarding the corresponding available cDNA clones and their structural properties. Because of these features, our database is unique and may provide useful information for systematic genome-wide studies of transcriptional regulation. (C) 2004 Elsevier Inc. All rights reserved.

引用

页码：787 / 793

页数：7

共 16 条

[1] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[2] A genomic regulatory network for development [J].

Davidson, EH ;

Rast, JP ;

Oliveri, P ;

Ransick, A ;

Calestani, C ;

Yuh, CH ;

Minokawa, T ;

Amore, G ;

Hinman, V ;

Arenas-Mena, C ;

Otim, O ;

Brown, CT ;

Livi, CB ;

Lee, PY ;

Revilla, R ;

Rust, AG ;

Pan, ZJ ;

Schilstra, MJ ;

Clarke, PJC ;

Arnone, MI ;

Rowen, L ;

Cameron, RA ;

McClay, DR ;

Hood, L ;

Bolouri, H .

SCIENCE, 2002, 295 (5560) :1669-1678

[3] Reflections on apparent DNA bending by charge variants of bZIP proteins [J].

Hardwidge, PR ;

Parkhurst, KM ;

Parkhurst, LJ ;

Maher, LJ .

BIOPOLYMERS, 2003, 69 (01) :110-117

[4] TrSDB: a proteome database of transcription factors [J].

Hermoso, A ;

Aguilar, D ;

Aviles, FX ;

Querol, E .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D171-D173

[5]

Hryniewicz-Jankowska A, 2002, FOLIA HISTOCHEM CYTO, V40, P239

[6] DNA book [J].

Kawai, J ;

Hayashizaki, Y .

GENOME RESEARCH, 2003, 13 (6B) :1488-1495

[7] Transcriptional regulatory networks in Saccharomyces cerevisiae [J].

Lee, TI ;

Rinaldi, NJ ;

Robert, F ;

Odom, DT ;

Bar-Joseph, Z ;

Gerber, GK ;

Hannett, NM ;

Harbison, CT ;

Thompson, CM ;

Simon, I ;

Zeitlinger, J ;

Jennings, EG ;

Murray, HL ;

Gordon, DB ;

Ren, B ;

Wyrick, JJ ;

Tagne, JB ;

Volkert, TL ;

Fraenkel, E ;

Gifford, DK ;

Young, RA .

SCIENCE, 2002, 298 (5594) :799-804

[8] Fox's in development and disease [J].

Lehmann, OJ ;

Sowden, JC ;

Carlsson, P ;

Jordan, T ;

Bhattacharya, SS .

TRENDS IN GENETICS, 2003, 19 (06) :339-344

[9] THE SPECIFICITY OF HOMEOTIC GENE-FUNCTION [J].

MANN, RS .

BIOESSAYS, 1995, 17 (10) :855-863

[10] Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs [J].

Okazaki, Y ;

Furuno, M ;

Kasukawa, T ;

Adachi, J ;

Bono, H ;

Kondo, S ;

Nikaido, I ;

Osato, N ;

Saito, R ;

Suzuki, H ;

Yamanaka, I ;

Kiyosawa, H ;

Yagi, K ;

Tomaru, Y ;

Hasegawa, Y ;

Nogami, A ;

Schönbach, C ;

Gojobori, T ;

Baldarelli, R ;

Hill, DP ;

Bult, C ;

Hume, DA ;

Quackenbush, J ;

Schriml, LM ;

Kanapin, A ;

Matsuda, H ;

Batalov, S ;

Beisel, KW ;

Blake, JA ;

Bradt, D ;

Brusic, V ;

Chothia, C ;

Corbani, LE ;

Cousins, S ;

Dalla, E ;

Dragani, TA ;

Fletcher, CF ;

Forrest, A ;

Frazer, KS ;

Gaasterland, T ;

Gariboldi, M ;

Gissi, C ;

Godzik, A ;

Gough, J ;

Grimmond, S ;

Gustincich, S ;

Hirokawa, N ;

Jackson, IJ ;

Jarvis, ED ;

Kanai, A .

NATURE, 2002, 420 (6915) :563-573

← 1 2 →