Gene Ontology term overlap as a measure of gene functional similarity

doi:10.1186/1471-2105-9-327

BMC Bioinformatics

Volume 9

Viewing options:

Abstract
Full text
PDF (3.7MB)
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

Mistry M
Pavlidis P

on PubMed

Mistry M
Pavlidis P
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Research article

Gene Ontology term overlap as a measure of gene functional similarity

Meeta Mistry¹ and Paul Pavlidis²

¹CIHR/MSFHR Graduate Program in Bioinformatics, University of British Columbia, Canada

²Department of Psychiatry and Centre for High-throughput Biology, University of British Columbia, British Columbia, Canada

author email corresponding author email

BMC Bioinformatics 2008, 9:327doi:10.1186/1471-2105-9-327


Published:	4 August 2008

Additional files

Additional File 1:

TO correlation scores for multiple sets.

Format: DOC Size: 37KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional File 2:

Correlation values amongst various similarity measures.

Format: DOC Size: 74KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional File 3:

TO scores versus scores generated using vector -based measures. For every gene pair in the 100 k set of gene pairs, the term overlap was calculated and plotted against the scores generated by Cosine, Kappa, and Weighted Cosine measures.

Format: DOC Size: 59KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional File 4:

NTO scores versus TO, Resnik, Lin, and Jiang scores. For every gene pair in the 100 k set of gene pairs, the normalized term overlap was calculated and plotted against the term overlap scores (A), the averaged variant scores of each of the three semantic similarity measures (B-D), and the maximum variant scores of each of the three semantic similarity measures (E-G).

Format: DOC Size: 187KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional File 5:

Comparing sequence and semantic similarity ("average" variants). A BLAST sequence analysis was carried out to calculate a sequence similarity score for each gene pair in the 100 k set for which sequence data was available. Of those gene pairs we considered only the 53,264 which obtained a score greater than zero. Intervals were taken along the x-axis ln [Bit Score] and (A) Resnik, (B) Lin and (C) Jiang scores for the corresponding gene pairs were averaged and plotted.

Format: DOC Size: 43KB Download file

This file can be viewed with: Microsoft Word Viewer