Identifying metabolic enzymes with multiple types of association evidence

doi:10.1186/1471-2105-7-177

BMC Bioinformatics

Volume 7

Viewing options:

Abstract
Full text
PDF (452KB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Kharchenko P
Chen L
Freund Y
Vitkup D
Church GM

on PubMed

Kharchenko P
Chen L
Freund Y
Vitkup D
Church GM
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Methodology article

Identifying metabolic enzymes with multiple types of association evidence

Peter Kharchenko¹ , Lifeng Chen² , Yoav Freund³ , Dennis Vitkup² and George M Church¹

¹Department of Genetics, New Research Building (NRB) Room 238, 77 Ave. Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA

²Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, 1150 St. Nicholas Ave., New York, NY 10032, USA

³Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive 0404, Room 4126, La Jolla, CA 92093, USA

author email corresponding author email

BMC Bioinformatics 2006, 7:177doi:10.1186/1471-2105-7-177


Published:	29 March 2006

Additional files

Additional File 1:

Performance of different profile similarity measures.

Format: PDF Size: 214KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 2:

Distribution of the number of orthologs per organism.

Format: PDF Size: 191KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 3:

Performance of different profile similarity measures.

Format: PDF Size: 223KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 4:

Paralogs and orthologs among metabolic enzymes.

Format: PDF Size: 255KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 5:

Performance bias due to paralogous metabolic enzymes.

Format: PDF Size: 264KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 6:

Ortholog co-expression performance.

Format: PDF Size: 229KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 7:

Performance of protein fusion associations.

Format: PDF Size: 243KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 8:

Self-rank performance of phenotypic profiles.

Format: PDF Size: 224KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 9:

Effects of metabolite weighting and association-rank rescaling corrections.

Format: PDF Size: 247KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 10:

Alternating decision trees and related structures.

Format: PDF Size: 474KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 11:

Overlap in predictions based on different types of association evidence.

Format: PDF Size: 268KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 12:

Performance of predictions based on KEGG pathway membership.

Format: PDF Size: 231KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 13:

Sensitivity of prediction performance on the choice of excluded metabolites.

Format: PDF Size: 224KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 15:

Prediction performance with and without paralog exclusion.

Format: PDF Size: 233KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 16:

Gene coverage of different orthology datasets. Additional datasets, including pair-wise functional association matrices for different types of evidence and BLAST-based orthology datasets, are available on the authors' web site[63].

Format: PDF Size: 14KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 14:

Chromosome clustering using Gene Order vs. Gene Nucleotide Position.

Format: PDF Size: 333KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 17:

predictions.zip. Sample predictions of E. coli orphans. Additional datasets, including pair-wise functional association matrices for different types of evidence and BLAST-based orthology datasets, are available on the authors' web site[63].

Format: ZIP Size: 2.6MB Download file