DBTSS: DataBase of Human Transcription Start Sites, progress report 2006

被引：80

作者：

Yamashita, Riu

Suzuki, Yutaka

Wakaguri, Hiroyuki

Tsuritani, Katsuki

Nakai, Kenta

Sugano, Sumio

机构：

[1] Univ Tokyo, Inst Med Sci, Ctr Human Genome, Minato Ku, Tokyo, Japan

[2] Univ Tokyo, Grad Sch Frontier Sci, Dept Med Genome Sci, Kashiwa, Chiba 2778562, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷

关键词：

D O I：

10.1093/nar/gkj129

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：

DBTSS was first constructed in 2002 based on precise, experimentally determined 5' end clones. Several major updates and additions have been made since the last report. First, the number of human clones has drastically increased, going from 190 964 to 1 359 000. Second, information about potential alternative promoters is presented because the number of 50 end clones is now sufficient to determine several promoters for one gene. Namely, we defined putative promoter groups by clustering transcription start sites (TSSs) separated by,500 bases. A total of 8308 human genes and 4276 mouse genes were found to have putative multiple promoters. Third, DBTSS provides detailed sequence comparisons of user-specified TSSs. Finally, we have added TSS information for zebrafish, malaria and schyzon (a red algae model organism). DBTSS is accessible at http://dbtss.hgc.jp.

引用

页码：D86 / D89

页数：4

共 18 条

[1] Promoter prediction analysis on the whole human genome [J].

Bajic, VB ;

Tan, SL ;

Suzuki, Y ;

Sugano, S .

NATURE BIOTECHNOLOGY, 2004, 22 (11) :1467-1473

[2] High-efficiency full-length cDNA cloning by biotinylated CAP trapper [J].

Carninci, P ;

Kvam, C ;

Kitamura, A ;

Ohsumi, T ;

Okazaki, Y ;

Itoh, M ;

Kamiya, M ;

Shibata, K ;

Sasaki, N ;

Izawa, M ;

Muramatsu, M ;

Hayashizaki, Y ;

Schneider, C .

GENOMICS, 1996, 37 (03) :327-336

[3]

Carninci P, 1997, DNA Res, V4, P61, DOI 10.1093/dnares/4.1.61

[4] GENOMIC SEQUENCES OF HUMAN PROTAMINES WHOSE GENES, PRM1 AND PRM2, ARE CLUSTERED [J].

DOMENJOUD, L ;

NUSSBAUM, G ;

ADHAM, IM ;

GREESKE, G ;

ENGEL, W .

GENOMICS, 1990, 8 (01) :127-133

[5]

Gerhard DS, 2004, GENOME RES, V14, P2121, DOI 10.1101/gr.2596504

[6]

HUANG XQ, 1992, COMPUT APPL BIOSCI, V8, P155

[7]

KIMURA K, 2005, IN PRESS GENOME RES

[8] Complex controls: the role of alternative promoters in mammalian genomes [J].

Landry, JR ;

Mager, DL ;

Wilhelm, BT .

TRENDS IN GENETICS, 2003, 19 (11) :640-648

[9]

MARUYAMA K, 1994, GENE, V138, P171

[10] Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D [J].

Matsuzaki, M ;

Misumi, O ;

Shin-I, T ;

Maruyama, S ;

Takahara, M ;

Miyagishima, SY ;

Mori, T ;

Nishida, K ;

Yagisawa, F ;

Nishida, K ;

Yoshida, Y ;

Nishimura, Y ;

Nakao, S ;

Kobayashi, T ;

Momoyama, Y ;

Higashiyama, T ;

Minoda, A ;

Sano, M ;

Nomoto, H ;

Oishi, K ;

Hayashi, H ;

Ohta, F ;

Nishizaka, S ;

Haga, S ;

Miura, S ;

Morishita, T ;

Kabeya, Y ;

Terasawa, K ;

Suzuki, Y ;

Ishii, Y ;

Asakawa, S ;

Takano, H ;

Ohta, N ;

Kuroiwa, H ;

Tanaka, K ;

Shimizu, N ;

Sugano, S ;

Sato, N ;

Nozaki, H ;

Ogasawara, N ;

Kohara, Y ;

Kuroiwa, T .

NATURE, 2004, 428 (6983) :653-657

← 1 2 →