TB database 2010: Overview and update

被引：90

作者：

Galagan, James E. ^{[1
,2
,3
]}

Sisk, Peter ^{[2
]}

Stolte, Christian ^{[2
]}

Weiner, Brian ^{[2
]}

Koehrsen, Michael ^{[2
]}

Wymore, Farrell ^{[4
]}

Reddy, T. B. K. ^{[4
]}

Zucker, Jeremy D. ^{[2
]}

Engels, Reinhard ^{[2
]}

Gellesch, Marcel ^{[2
]}

Hubble, Jeremy ^{[5
]}

Jin, Heng ^{[4
]}

Larson, Lisa ^{[2
]}

Mao, Maria ^{[5
]}

Nitzberg, Michael ^{[4
]}

White, Jared ^{[2
]}

Zachariah, Zachariah K. ^{[4
]}

Sherlock, Gavin ^{[5
]}

Ball, Catherine A. ^{[4
]}

Schoolnik, Gary K. ^{[6
]}

机构：

[1] Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

[2] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[3] Boston Univ, Natl Emerging Infect Dis Lab, Boston, MA 02118 USA

[4] Stanford Univ, Dept Biochem, Sch Med, Stanford, CA 94305 USA

[5] Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA

[6] Stanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA

来源：

TUBERCULOSIS | 2010年 / 90卷 / 04期

关键词：

Tuberculosis; Database; Genome; Microarray; Diversity; MYCOBACTERIUM-TUBERCULOSIS; OPERON PREDICTION; GENES; SEQUENCE; ARCHIVE; TOOL;

D O I：

10.1016/j.tube.2010.03.010

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

摘要：

The Tuberculosis Database (TBDB) is an online database providing integrated access to genome sequence, expression data and literature curation for TB. TBDB currently houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. We provide here an overview of TBDB focusing on recent data releases and enhancements. In particular, we describe the recent release of a Global Genetic Diversity dataset for TB, support for short-read re-sequencing data, new tools for exploring gene expression data in the context of gene regulation, and the integration of a metabolic network reconstruction and BioCyc with TBDB. By integrating a wide range of genomic data with tools for their use, TBDB is a unique platform for both basic science research in TB, as well as research into the discovery and development of TB drugs, vaccines and biomarkers. (C) 2010 Elsevier Ltd. All rights reserved.

引用

页码：225 / 235

页数：11

共 22 条

[1] 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

[2] NCBI GEO: archive for high-throughput functional genomic data [J].

Barrett, Tanya ;

Troup, Dennis B. ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Rudnev, Dmitry ;

Evangelista, Carlos ;

Kim, Irene F. ;

Soboleva, Alexandra ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Muertter, Rolf N. ;

Edgar, Ron .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D885-D890

[3] GSMN-TB:: a web-based genome scale network model of Mycobacterium tuberculosis metabolism [J].

Beste, Dany J. V. ;

Hooper, Tracy ;

Stewart, Graham ;

Bonde, Bushan ;

Avignone-Rossa, Claudio ;

Bushell, Michael ;

Wheeler, Paul ;

Klamt, Steffen ;

Kierzek, Andrzej M. ;

McFadden, Johnjoe .

GENOME BIOLOGY, 2007, 8 (05)

[4]

Craven M, 2000, Proc Int Conf Intell Syst Mol Biol, V8, P116

[5] A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context [J].

Edwards, MT ;

Rison, SCG ;

Stoker, NG ;

Wernisch, L .

NUCLEIC ACIDS RESEARCH, 2005, 33 (10) :3253-3262

[6] Pfam:: clans, web tools and services [J].

Finn, Robert D. ;

Mistry, Jaina ;

Schuster-Bockler, Benjamin ;

Griffiths-Jones, Sam ;

Hollich, Volker ;

Lassmann, Timo ;

Moxon, Simon ;

Marshall, Mhairi ;

Khanna, Ajay ;

Durbin, Richard ;

Eddy, Sean R. ;

Sonnhammer, Erik L. L. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D247-D251

[7] Rfam: updates to the RNA families database [J].

Gardner, Paul P. ;

Daub, Jennifer ;

Tate, John G. ;

Nawrocki, Eric P. ;

Kolbe, Diana L. ;

Lindgreen, Stinus ;

Wilkinson, Adam C. ;

Finn, Robert D. ;

Griffiths-Jones, Sam ;

Eddy, Sean R. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D136-D140

[8]

Giglia E, 2009, Eur J Phys Rehabil Med, V45, P155

[9] High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography [J].

Hershberg, Ruth ;

Lipatov, Mikhail ;

Small, Peter M. ;

Sheffer, Hadar ;

Niemann, Stefan ;

Homolka, Susanne ;

Roach, Jared C. ;

Kremer, Kristin ;

Petrov, Dmitri A. ;

Feldman, Marcus W. ;

Gagneux, Sebastien .

PLOS BIOLOGY, 2008, 6 (12) :2658-2671

[10] Implementation of GenePattern within the Stanford Microarray Database [J].

Hubble, Jeremy ;

Demeter, Janos ;

Jin, Heng ;

Mao, Maria ;

Nitzberg, Michael ;

Reddy, T. B. K. ;

Wymore, Farrell ;

Zachariah, K. ;

Sherlock, Gavin ;

Ball, Catherine A. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D898-D901

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