Assessing computational tools for the discovery of transcription factor binding sites

被引：844

作者：

Tompa, M

Li, N

Bailey, TL

Church, GM

De Moor, B

Eskin, E

Favorov, AV

Frith, MC

Fu, YT

Kent, WJ

Makeev, VJ

Mironov, AA

Noble, WS

Pavesi, G

Pesole, G

Régnier, M

Simonis, N

Sinha, S

Thijs, G

van Helden, J

Vandenbogaert, M

Weng, ZP

Workman, C

Ye, C

Zhu, Z

机构：

[1] Univ Washington, Dept Comp Sci & Engn, Seattle, WA 98195 USA

[2] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[3] Univ Queensland, Inst Mol Biosci, Brisbane, Qld, Australia

[4] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[5] Harvard Univ, Sch Med, Lipper Ctr Computat Genet, Boston, MA 02115 USA

[6] Katholieke Univ Leuven, ESAT SCD, B-3001 Louvain, Belgium

[7] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[8] State Sci Ctr GosNIIGenet, Moscow 117545, Russia

[9] Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia

[10] Boston Univ, Bioinformat Program, Boston, MA 02215 USA

[11] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[12] Moscow MV Lomonosov State Univ, Dept Bioengn & Bioinformat, Moscow 119992, Russia

[13] Univ Milan, Dept Comp Sci & Commun DICo, Milan, Italy

[14] Univ Milan, Dept Biomol Sci & Biotechnol, Milan, Italy

[15] INRIA Rocquencourt, F-78153 Le Chesnay, France

[16] Free Univ Brussels, SCMB, B-1050 Brussels, Belgium

[17] Rockefeller Univ, Ctr Studies Phys & Biol, New York, NY 10021 USA

[18] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[19] Univ Calif San Diego, Bioinformat Program, La Jolla, CA 92093 USA

来源：

NATURE BIOTECHNOLOGY | 2005年 / 23卷 / 01期

关键词：

D O I：

10.1038/nbt1053

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：

The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

引用

页码：137 / 144

页数：8

共 50 条

[31] Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility
Sheng Liu
Cristina Zibetti
Jun Wan
Guohua Wang
Seth Blackshaw
Jiang Qian
BMC Bioinformatics, 18
[32] Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility
Liu, Sheng
Zibetti, Cristina
Wan, Jun
Wang, Guohua
Blackshaw, Seth
Qian, Jiang
BMC BIOINFORMATICS, 2017, 18
[33] Whole-genome discovery of transcription factor binding sites by network-level conservation
Pritsker, M
Liu, YC
Beer, MA
Tavazoie, S
GENOME RESEARCH, 2004, 14 (01) : 99 - 108
[34] The Robustness and Evolvability of Transcription Factor Binding Sites
Payne, Joshua L.
Wagner, Andreas
SCIENCE, 2014, 343 (6173) : 875 - 877
[35] Evolution of transcription factor DNA binding sites
Kotelnikova, EA
Makeev, VJ
Gelfand, MS
GENE, 2005, 347 (02) : 255 - 263
[36] Assessing computational tools for the discovery of small RNA genes in bacteria
Lu, Xiaojun
Goodrich-Blair, Heidi
Tjaden, Brian
RNA, 2011, 17 (09) : 1635 - 1647
[37] Adaptive evolution of transcription factor binding sites
Johannes Berg
Stana Willmann
Michael Lässig
BMC Evolutionary Biology, 4
[38] Position dependencies in transcription factor binding sites
Tomovic, Andrija
Oakeley, Edward J.
BIOINFORMATICS, 2007, 23 (08) : 933 - 941
[39] Genetic Variation in Transcription Factor Binding Sites
Santpere, Gabriel
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2023, 24 (05)
[40] MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
Marinescu, VD
Kohane, IS
Riva, A
BMC BIOINFORMATICS, 2005, 6 (1)

← 1 2 3 4 5 →