TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs

被引：58

作者：

Gordon, DB

Nekludova, L

McCallum, S

Fraenkel, E

机构：

[1] Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

[2] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA

来源：

BIOINFORMATICS | 2005年 / 21卷 / 14期

关键词：

D O I：

10.1093/bioinformatics/bti481

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

TAMO ( Tools for Analysis of MOtifs) is an object-oriented computational framework for interpreting transcriptional regulation using DNA-sequence motifs. To simplify the application of multiple motif discovery programs to genome-wide data, TAMO provides a sophisticated motif object with interfaces to several popular programs. In addition, TAMO provides modules for integrating motif analysis with diverse data sources including genomic sequences, microarrays and various databases. Finally, TAMO includes tools for sequence analysis, algorithms for scoring, comparing and clustering motifs, and several useful statistical tests. Recently, we have applied these tools to analyze tens of thousands of motifs derived from hundreds of microarray experiments.

引用

页码：3164 / 3165

页数：2

共 11 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]

Bailey T L, 1995, Proc Int Conf Intell Syst Mol Biol, V3, P21

[3] Genetic and physical maps of Saccharomyces cerevisiae [J].

Cherry, JM ;

Ball, C ;

Weng, S ;

Juvik, G ;

Schmidt, R ;

Adler, C ;

Dunn, B ;

Dwight, S ;

Riles, L ;

Mortimer, RK ;

Botstein, D .

NATURE, 1997, 387 (6632) :67-73

[4] Rank order metrics for quantifying the association of sequence features with gene regulation [J].

Clarke, ND ;

Granek, JA .

BIOINFORMATICS, 2003, 19 (02) :212-218

[5] Transcriptional regulatory code of a eukaryotic genome [J].

Harbison, CT ;

Gordon, DB ;

Lee, TI ;

Rinaldi, NJ ;

Macisaac, KD ;

Danford, TW ;

Hannett, NM ;

Tagne, JB ;

Reynolds, DB ;

Yoo, J ;

Jennings, EG ;

Zeitlinger, J ;

Pokholok, DK ;

Kellis, M ;

Rolfe, PA ;

Takusagawa, KT ;

Lander, ES ;

Gifford, DK ;

Fraenkel, E ;

Young, RA .

NATURE, 2004, 431 (7004) :99-104

[6] Dissecting the regulatory circuitry of a eukaryotic genome [J].

Holstege, FCP ;

Jennings, EG ;

Wyrick, JJ ;

Lee, TI ;

Hengartner, CJ ;

Green, MR ;

Golub, TR ;

Lander, ES ;

Young, RA .

CELL, 1998, 95 (05) :717-728

[7] Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae [J].

Hughes, JD ;

Estep, PW ;

Tavazoie, S ;

Church, GM .

JOURNAL OF MOLECULAR BIOLOGY, 2000, 296 (05) :1205-1214

[8] The UCSC Genome Browser Database [J].

Karolchik, D ;

Baertsch, R ;

Diekhans, M ;

Furey, TS ;

Hinrichs, A ;

Lu, YT ;

Roskin, KM ;

Schwartz, M ;

Sugnet, CW ;

Thomas, DJ ;

Weber, RJ ;

Haussler, D ;

Kent, WJ .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :51-54

[9] An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments [J].

Liu, XS ;

Brutlag, DL ;

Liu, JS .

NATURE BIOTECHNOLOGY, 2002, 20 (08) :835-839

[10] A gene atlas of the mouse and human protein-encoding transcriptomes [J].

Su, AI ;

Wiltshire, T ;

Batalov, S ;

Lapp, H ;

Ching, KA ;

Block, D ;

Zhang, J ;

Soden, R ;

Hayakawa, M ;

Kreiman, G ;

Cooke, MP ;

Walker, JR ;

Hogenesch, JB .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (16) :6062-6067

← 1 2 →