Skip Navigation


Bioinformatics Advance Access originally published online on June 9, 2004
Bioinformatics 2004 20(17):2973-2984; doi:10.1093/bioinformatics/bth342
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/17/2973    most recent
bth342v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 ISI Web of Science
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 Search for citing articles in:
ISI Web of Science (23)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Wang, J.-P. Z.
Right arrow Articles by dePamphilis, C. W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wang, J.-P. Z.
Right arrow Articles by dePamphilis, C. W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

EST clustering error evaluation and correction

Ji-Ping Z. Wang 1,2,*, Bruce G. Lindsay 2, James Leebens-Mack 3, Liying Cui 3, Kerr Wall 3, Webb C. Miller 3 and Claude W. dePamphilis 3

1 Department of Statistics, Northwestern University, Evanston, IL 60208, USA, 2 Department of Statistics and 3 Department of Biology, Pennsylvania State University, University Park, PA 16802, USA

Received on February 23, 2004; revised on May 13, 2004; accepted on May 18, 2004
Advance Access Publication June 9, 2004

Motivation: The gene expression intensity information conveyed by (EST) Expressed Sequence Tag data can be used to infer important cDNA library properties, such as gene number and expression patterns. However, EST clustering errors, which often lead to greatly inflated estimates of obtained unique genes, have become a major obstacle in the analyses. The EST clustering error structure, the relationship between clustering error and clustering criteria, and possible error correction methods need to be systematically investigated.

Results: We identify and quantify two types of EST clustering error, namely, Type I and II in EST clustering using CAP3 assembling program. A Type I error occurs when ESTs from the same gene do not form a cluster whereas a Type II error occurs when ESTs from distinct genes are falsely clustered together. While the Type II error rate is <1.5% for both 5' and 3' EST clustering, the Type I error in the 5' EST case is ~10 times higher than the 3' EST case (30% versus 3%). An over-stringent identity rule, e.g., P ≥ 95%, may even inflate the Type I error in both cases. We demonstrate that ~80% of the Type I error is due to insufficient overlap among sibling ESTs (ISO error) in 5' EST clustering. A novel statistical approach is proposed to correct ISO error to provide more accurate estimates of the true gene cluster profile.

Availability: We have automated the methods developed in this paper in a web-based software ESTstat at http://cwdg5.bio.psu.edu/eststat.

Supplementary information: http://cwdg5.bio.psu.edu/eststat

Contact: jzwang{at}northwestern.edu

* To whom correspondence should be addressed.


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
 BioinformaticsHome page
L. M. Bragg and G. Stone
k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage
Bioinformatics, September 15, 2009; 25(18): 2302 - 2308.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
F. C. Almeida and R. DeSalle
Orthology, Function and Evolution of Accessory Gland Proteins in the Drosophila repleta Group
Genetics, January 1, 2009; 181(1): 235 - 245.
[Abstract] [Full Text] [PDF]

Home page
 Biol. Bull.Home page
R. M. Freeman JR., M. Wu, M-M. Cordonnier-Pratt, L. H. Pratt, C. E. Gruber, M. Smith, E. S. Lander, N. Stange-Thomann, C. J. Lowe, J. Gerhart, et al.
cDNA Sequences for Transcription Factors and Signaling Proteins of the Hemichordate Saccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism
Biol. Bull., June 1, 2008; 214(3): 284 - 302.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
S. H. Nagaraj, R. B. Gasser, and S. Ranganathan
A hitchhiker's guide to expressed sequence tag (EST) analysis
Brief Bioinform, January 1, 2007; 8(1): 6 - 21.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Malde, K. Schneeberger, E. Coward, and I. Jonassen
RBR: library-less repeat detection for ESTs
Bioinformatics, September 15, 2006; 22(18): 2232 - 2236.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L. Cui, P. K. Wall, J. H. Leebens-Mack, B. G. Lindsay, D. E. Soltis, J. J. Doyle, P. S. Soltis, J. E. Carlson, K. Arumuganathan, A. Barakat, et al.
Widespread genome duplications throughout the history of flowering plants
Genome Res., June 1, 2006; 16(6): 738 - 749.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
L. H. Pratt, C. Liang, M. Shah, F. Sun, H. Wang, St. P. Reid, A. R. Gingle, A. H. Paterson, R. Wing, R. Dean, et al.
Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis, and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts
Plant Physiology, October 1, 2005; 139(2): 869 - 884.
[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.