By Topic

A New Path Length Measure Based on GO for Gene Similarity with Evaluation using SGD Pathways

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$33 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

2 Author(s)
Anurag Nagar ; Univ. of Houston-Clear Lake, Houston, TX ; Hisham Al-Mubaid

We propose a new method for measuring the semantic similarity of genes based on path length between their annotation terms in the gene ontology. Our method applies an exponential transfer function to the average path length between two genes to compute their similarity. The non-linear measure ensures that the semantic similarity decreases with distance and proves to be quite competitive when compared to other measures. The advantage of the proposed measure is its simplicity and ease of implementation which gives it a great appeal in this domain. The measure uses only one feature (path length) for computing the similarity between genes. For validation purposes, we computed the similarity of genes from the Saccharomyces genome database (SGD) taking part in various cellular pathways. We analyzed 152 pathways from SGD and compared our similarity results with two of the leading measures. The proposed measure proved to be very competitive in all cases and the clustering results showed that our method is able to surpass the leading methods in certain cases.

Published in:

Computer-Based Medical Systems, 2008. CBMS '08. 21st IEEE International Symposium on

Date of Conference:

17-19 June 2008