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

Content Provider	IEEE Xplore Digital Library
Author	Nagar, A. Al-Mubaid, H.
Copyright Year	2008
Description	Author affiliation: Univ. of Houston-Clear Lake, Houston, TX (Nagar, A.; Al-Mubaid, H.)
Abstract	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.
Starting Page	590
Ending Page	595
File Size	507255
Page Count	6
File Format	PDF
ISBN	9780769531656
ISSN	10637125
DOI	10.1109/CBMS.2008.27
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-06-17
Publisher Place	Finland
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Length measurement Ontologies Bioinformatics Databases Genomics Organisms Lakes USA Councils Collaboration Transfer functions Gene Similarity in SGD Gene similarity GO term similarity
Content Type	Text
Resource Type	Article
Subject	Radiology, Nuclear Medicine and Imaging Computer Science Applications

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in