Skip Navigation

Nucleic Acids Research 2006 34(Database Issue):D731-D735; doi:10.1093/nar/gkj077
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1963K) Freely available
Right arrow Screen PDF (270K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Nakano, M.
Right arrow Articles by Meyers, B. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nakano, M.
Right arrow Articles by Meyers, B. C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2006, Vol. 34, Database issue D731-D735
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA

Mayumi Nakano1, Kan Nobuta1, Kalyan Vemaraju2, Shivakundan Singh Tej2, Jeremy W. Skogen2 and Blake C. Meyers1,2,*

1Department of Plant and Soil Sciences, University of Delaware Newark, DE 19714, USA 2Delaware Biotechnology Institute, University of Delaware Newark, DE 19714, USA

*To whom correspondence should be addressed. Tel: +1 302 831 3418; Fax: +1 302 831 4841; Email: meyers{at}dbi.udel.edu

Received August 15, 2005. Revised October 11, 2005. Accepted October 11, 2005.

MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We have created a series of databases for four species (Arabidopsis, rice, grape and Magnaporthe grisea, the rice blast fungus). Our MPSS databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms and regulatory intergenic transcripts). A modified version of MPSS has been used to perform deep profiling of small RNAs from Arabidopsis, and we have recently adapted our database to display these data. Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at http://mpss.udel.edu.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol PlantHome page
C. Fan, Y. Zhang, Y. Yu, S. Rounsley, M. Long, and R. A. Wing
The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice
Mol Plant, August 22, 2008; (2008) ssn050v1.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
R. D. Morin, M. D. O'Connor, M. Griffith, F. Kuchenbauer, A. Delaney, A.-L. Prabhu, Y. Zhao, H. McDonald, T. Zeng, M. Hirst, et al.
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
Genome Res., April 1, 2008; 18(4): 610 - 621.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
R. D. Morin, G. Aksay, E. Dolgosheina, H. A. Ebhardt, V. Magrini, E. R. Mardis, S. C. Sahinalp, and P. J. Unrau
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
Genome Res., April 1, 2008; 18(4): 571 - 584.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
Y. Tagami, N. Inaba, N. Kutsuna, Y. Kurihara, and Y. Watanabe
Specific Enrichment of miRNAs in Arabidopsis thaliana Infected with Tobacco mosaic virus
DNA Res, December 1, 2007; (2007) dsm022v1.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. Menges, G. Pavesi, P. Morandini, L. Bogre, and J. A.H. Murray
Genomic Organization and Evolutionary Conservation of Plant D-Type Cyclins
Plant Physiology, December 1, 2007; 145(4): 1558 - 1576.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. A. Johnson and M. A. Thomas
The Monosaccharide Transporter Gene Family in Arabidopsis and Rice: A History of Duplications, Adaptive Evolution, and Functional Divergence
Mol. Biol. Evol., November 1, 2007; 24(11): 2412 - 2423.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
N. A. Eckardt
Positive and Negative Feedback Coordinate Regulation of Disease Resistance Gene Expression
PLANT CELL, September 1, 2007; 19(9): 2700 - 2702.
[Full Text] [PDF]

Home page
 Plant CellHome page
H. Yi and E. J. Richards
A Cluster of Disease Resistance Genes in Arabidopsis Is Coordinately Regulated by Transcriptional Activation and RNA Silencing
PLANT CELL, September 1, 2007; 19(9): 2929 - 2939.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
A. P.M. Weber, K. L. Weber, K. Carr, C. Wilkerson, and J. B. Ohlrogge
Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing
Plant Physiology, May 1, 2007; 144(1): 32 - 42.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
C. Dardick, J. Chen, T. Richter, S. Ouyang, and P. Ronald
The Rice Kinase Database. A Phylogenomic Database for the Rice Kinome
Plant Physiology, February 1, 2007; 143(2): 579 - 586.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Ouyang, W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibaud-Nissen, R. L. Malek, Y. Lee, L. Zheng, et al.
The TIGR Rice Genome Annotation Resource: improvements and new features
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D883 - D887.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. A. Lease and J. C. Walker
The Arabidopsis Unannotated Secreted Peptide Database, a Resource for Plant Peptidomics
Plant Physiology, November 1, 2006; 142(3): 831 - 838.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
X. Li, X. Duan, H. Jiang, Y. Sun, Y. Tang, Z. Yuan, J. Guo, W. Liang, L. Chen, J. Yin, et al.
Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis
Plant Physiology, August 1, 2006; 141(4): 1167 - 1184.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. R. Hoen, K. C. Park, N. Elrouby, Z. Yu, N. Mohabir, R. K. Cowan, and T. E. Bureau
Transposon-Mediated Expansion and Diversification of a Family of ULP-like Genes
Mol. Biol. Evol., June 1, 2006; 23(6): 1254 - 1268.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.