UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

被引：108

作者：

Robasky, Kimberly ^{[1
,2
]}

Bulyk, Martha L. ^{[1
,3
,4
]}

机构：

[1] Brigham & Womens Hosp, Dept Med, Div Genet, Boston, MA 02115 USA

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

[3] Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA

[4] Harvard Univ, Sch Med, Harvard MIT Div Hlth Sci & Technol HST, Boston, MA 02115 USA

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

美国国家卫生研究院;

关键词：

SPECIFICITIES; RECOGNITION; NETWORK;

D O I：

10.1093/nar/gkq992

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：

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe > 130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.

引用

页码：D124 / D128

页数：5

共 21 条

[1] Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example [J].

Alibes, Andreu ;

Nadra, Alejandro D. ;

De Masi, Federico ;

Bulyk, Martha L. ;

Serrano, Luis ;

Stricher, Francois .

NUCLEIC ACIDS RESEARCH, 2010, 38 (21) :7422-7431

[2] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[3] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[4] Diversity and Complexity in DNA Recognition by Transcription Factors [J].

Badis, Gwenael ;

Berger, Michael F. ;

Philippakis, Anthony A. ;

Talukder, Shaheynoor ;

Gehrke, Andrew R. ;

Jaeger, Savina A. ;

Chan, Esther T. ;

Metzler, Genita ;

Vedenko, Anastasia ;

Chen, Xiaoyu ;

Kuznetsov, Hanna ;

Wang, Chi-Fong ;

Coburn, David ;

Newburger, Daniel E. ;

Morris, Quaid ;

Hughes, Timothy R. ;

Bulyk, Martha L. .

SCIENCE, 2009, 324 (5935) :1720-1723

[5] Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences [J].

Berger, Michael F. ;

Badis, Gwenael ;

Gehrke, Andrew R. ;

Talukder, Shaheynoor ;

Philippakis, Anthony A. ;

Pena-Castillo, Lourdes ;

Alleyne, Trevis M. ;

Mnaimneh, Sanie ;

Botvinnik, Olga B. ;

Chan, Esther T. ;

Khalid, Faiqua ;

Zhang, Wen ;

Newburger, Daniel ;

Jaeger, Savina A. ;

Morris, Quaid D. ;

Bulyk, Martha L. ;

Hughes, Timothy R. .

CELL, 2008, 133 (07) :1266-1276

[6] Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities [J].

Berger, Michael F. ;

Philippakis, Anthony A. ;

Qureshi, Aaron M. ;

He, Fangxue S. ;

Estep, Preston W., III ;

Bulyk, Martha L. .

NATURE BIOTECHNOLOGY, 2006, 24 (11) :1429-1435

[7]

Bulyk ML, 2004, GENOME BIOL, V5

[8] Exploring the DNA-binding specificities of zinc fingers with DNA microarrays [J].

Bulyk, ML ;

Huang, XH ;

Choo, Y ;

Church, GM .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (13) :7158-7163

[9] Specific DNA-binding by Apicomplexan AP2 transcription factors [J].

De Silva, Erandi K. ;

Gehrke, Andrew R. ;

Olszewski, Kellen ;

Leon, Ilsa ;

Chahal, Jasdave S. ;

Bulyk, Martha L. ;

Llinas, Manuel .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (24) :8393-8398

[10] A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors [J].

Grove, Christian A. ;

De Masi, Federico ;

Barrasa, M. Inmaculada ;

Newburger, Daniel E. ;

Alkema, Mark J. ;

Bulyk, Martha L. ;

Walhout, Albertha J. M. .

CELL, 2009, 138 (02) :314-327

← 1 2 3 →