Genome-wide promoter extraction and analysis in human, mouse, and rat

被引：51

作者：

Xuan, ZY ^{[1
]}

Zhao, F ^{[1
]}

Wang, JH ^{[1
]}

Chen, GX ^{[1
]}

Zhang, MQ ^{[1
]}

机构：

[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

来源：

GENOME BIOLOGY | 2005年 / 6卷 / 08期

关键词：

D O I：

10.1186/gb-2005-6-8-r72

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Large-scale and high-throughput genomics research needs reliable and comprehensive genome-wide promoter annotation resources. We have conducted a systematic investigation on how to improve mammalian promoter prediction by incorporating both transcript and conservation information. This enabled us to build a better multispecies promoter annotation pipeline and hence to create CSHLmpd (Cold Spring Harbor Laboratory Mammalian Promoter Database) for the biomedical research community, which can act as a starting reference system for more refined functional annotations.

引用

页数：12

共 39 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]

Benson DA, 2003, NUCLEIC ACIDS RES, V31, P23, DOI 10.1093/nar/gkg057

[3] The European Bioinformatics Institute's data resources [J].

Brooksbank, C ;

Camon, E ;

Harris, MA ;

Magrane, M ;

Martin, MJ ;

Mulder, N ;

O'Donovan, C ;

Parkinson, H ;

Tuli, MA ;

Apweiler, R ;

Birney, E ;

Brazma, A ;

Henrick, K ;

Lopez, R ;

Stoesser, G ;

Stoehr, P ;

Cameron, G .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :43-50

[4] LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA [J].

Brudno, M ;

Do, CB ;

Cooper, GM ;

Kim, MF ;

Davydov, E ;

Green, ED ;

Sidow, A ;

Batzoglou, S .

GENOME RESEARCH, 2003, 13 (04) :721-731

[5] Experimental analysis of the annotation of promoters in the public database [J].

Coleman, SL ;

Buckland, PR ;

Hoogendoorn, B ;

Guy, C ;

Smith, K ;

O'Donovan, MC .

HUMAN MOLECULAR GENETICS, 2002, 11 (16) :1817-1821

[6]

*CSHL, CSHL MAMM PROM DAT C

[7] Computational identification of promoters and first exons in the human genome [J].

Davuluri, RV ;

Grosse, I ;

Zhang, MQ .

NATURE GENETICS, 2001, 29 (04) :412-417

[8] SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data [J].

Diehn, M ;

Sherlock, G ;

Binkley, G ;

Jin, H ;

Matese, JC ;

Hernandez-Boussard, T ;

Rees, CA ;

Cherry, JM ;

Botstein, D ;

Brown, PO ;

Alizadeh, AA .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :219-223

[9] The mouse genome: Experimental examination of gene predictions and transcriptional start sites [J].

Dike, S ;

Balija, VS ;

Nascimento, LU ;

Xuan, ZY ;

Ou, J ;

Zutavern, T ;

Palmer, LE ;

Hannon, G ;

Zhang, MQ ;

McCombie, WR .

GENOME RESEARCH, 2004, 14 (12) :2424-2429

[10] A computer program for aligning a cDNA sequence with a genomic DNA sequence [J].

Florea, L ;

Hartzell, G ;

Zhang, Z ;

Rubin, GM ;

Miller, W .

GENOME RESEARCH, 1998, 8 (09) :967-974

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