NDLI: A new path based hybrid measure for gene ontology similarity

Content Provider	ACM Digital Library
Author	Mallick, Koushik Bandyopadhyay, Sanghamitra
Copyright Year	2014
Abstract	Gene Ontology (GO) consists of a controlled vocabulary of terms, annotating a gene or gene product, structured in a directed acyclic graph. In the graph, semantic relations connect the terms, that represent the knowledge of functional description and cellular component information of gene products. GO similarity gives us a numerical representation of biological relationship between a gene set, which can be used to infer various biological facts such as protein interaction, structural similarity, gene clustering, etc. Here we introduce a new shortest path based hybrid measure of ontological similarity between two terms which combines both structure of the GO graph and information content of the terms. Here the similarity between two terms $\textit{t}1$ and $\textit{t}2,$ referred to as GOSimPBHM(t1, t2), has two components; one obtained from the common ancestors of $\textit{t}1$ and $\textit{t}2.$ The other from their remaining ancestors. The proposed path based hybrid measure does not suffer from the well-known shallow annotation problem. Its superiority with respect to some other popular measures is established for protein protein interaction prediction, correlation with gene expression and functional classification of genes in a biological pathway. Finally, the proposed measure is utilized to compute the average GO similarity score among the genes that are experimentally validated targets of some microRNAs. Results demonstrate that the targets of a given miRNA have a high degree of similarity in the biological process category of GO.
Starting Page	116
Ending Page	127
Page Count	12
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2013.149
Volume Number	11
Issue Number	1
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-01-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Functional classification of genes Gene ontology similarity Information content MicroRNA Protein interaction prediction Semantic similarity Term similarity
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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

A New Path Based Hybrid Measure for Gene Ontology Similarity

A New Path Based Hybrid Measure for Gene Ontology Similarity

A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms

Measure the semantic similarity of GO terms using aggregate information content

A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms

Semantic similarity measures on different ontologies: survey and a proposal of cross ontology based similarity measure (2013)

Departamento de inform ática improving semantic similarity for proteins based on the gene ontology.

A new semantic functional similarity over gene ontology

Measure the Semantic Similarity of GO Terms Using Aggregate Information Content

A new path based hybrid measure for gene ontology similarity

Similar Documents

A New Path Based Hybrid Measure for Gene Ontology Similarity

A New Path Based Hybrid Measure for Gene Ontology Similarity

A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms

Measure the semantic similarity of GO terms using aggregate information content

A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms

Semantic similarity measures on different ontologies: survey and a proposal of cross ontology based similarity measure (2013)

Departamento de inform ática improving semantic similarity for proteins based on the gene ontology.

A new semantic functional similarity over gene ontology

Measure the Semantic Similarity of GO Terms Using Aggregate Information Content

A new path based hybrid measure for gene ontology similarity