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Novel semantic similarity measure improves an integrative approach to predicting gene functional associations

Fatemeh Vafaee, Daniela Rosu, Fiona Broackes-Carter, Igor Jurisica
2013 BMC Systems Biology  
GAP integrates different biological features using a novel taxonomy-based semantic similarity measure in predicting and prioritizing high-quality putative gene associations.  ...  We present GAP (Gene functional Association Predictor), an integrative method for predicting and characterizing gene functional associations.  ...  We propose an integrative method, called Gene functional Association Predictor (GAP), which calculates a quantitative measure of gene functional relatedness, using a novel semantic similarity measure that  ... 
doi:10.1186/1752-0509-7-22 pmid:23497449 pmcid:PMC3663825 fatcat:dheiggdiojax5b44p6rv6zqa2q

Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies [article]

Susana Nunes, Rita T. Sousa, Catia Pesquita
2021 arXiv   pre-print
Ontology-based approaches for predicting gene-disease associations include the more classical semantic similarity methods and more recently knowledge graph embeddings.  ...  While semantic similarity is typically restricted to hierarchical relations within the ontology, knowledge graph embeddings consider their full breadth.  ...  In this study, we have proposed a novel approach to predict gene-disease associations using rich semantic representations based on KGEs over multiple ontologies.  ... 
arXiv:2105.04944v2 fatcat:m7niffgjlnfklk65rqfhnizipa

Ontology-based disease similarity network for disease gene prediction

Duc-Hau Le, Vu-Tung Dang
2016 Vietnam Journal of Computer Science  
., a controlled vocabulary database) and semantic similarity measures can be used to calculate similarities among them.  ...  Experiment results show that the ontology-based disease similarity network much improves the prediction performance compared to the one based on OMIM records, irrespective of gene/protein networks.  ...  In this study, we extended the use of RWRH algorithm to the prediction of disease-associated gene by integrating semantic similarities among diseases and a gene/protein network.  ... 
doi:10.1007/s40595-016-0063-3 fatcat:p7pa6y46ezetbg4brx3bziargq

IRWRLDA: improved random walk with restart for lncRNA-disease association prediction

Xing Chen, Zhu-Hong You, Gui-Ying Yan, Dun-Wei Gong
2016 OncoTarget  
lncRNA-disease associations by integrating known lncRNA-disease associations, disease semantic similarity, and various lncRNA similarity measures.  ...  Considering the limitations of traditional Random Walk with Restart (RWR), the model of Improved Random Walk with Restart for LncRNA-Disease Association prediction (IRWRLDA) was developed to predict novel  ...  Here, the model of Improved Random Walk with Restart for LncRNA-Disease Association prediction (IRWRLDA) was developed to predict novel lncRNAdisease associations by integrating known lncRNAdisease associations  ... 
doi:10.18632/oncotarget.11141 pmid:27517318 pmcid:PMC5295400 fatcat:xsqw5w76tjbsfh5usbf7wioaam

As Ontologies Reach Maturity, Artificial Intelligence Starts Being Fully Efficient: Findings from the Section on Knowledge Representation and Management for the Yearbook 2018

Jean Charlet, Ferdinand Dhombres
2018 IMIA Yearbook of Medical Informatics  
for 2018 demonstrate even further the added-value of ontology-based integration approaches for phenotype-genotype association mining.  ...  Conclusions: Ontologies are demonstrating their maturity to integrate medical data and begin to support clinical practices.  ...  Acknowledgements We would like to thank Martina Hutter and Adrien Ugon for their support and the reviewers for their participation in the selection process of best papers for the IMIA Yearbook.  ... 
doi:10.1055/s-0038-1667078 pmid:30157517 fatcat:otwpqzgeang5to4l7xfpiaf6ra

Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology [article]

Muhammad Asif, Hugo F. M. C. M. Martiniano, Astrid M. Vicente, Francisco M. Couto
2018 biorxiv/medrxiv   pre-print
A quantitative measure of gene functional similarities was obtained by employing different semantic similarity measures.  ...  a quantitative measure of gene functional similarities.  ...  Acknowledgments We would like to thank Ana Rita Marques and André Lamúrias for their valuable suggestions to improve this work. Author Contributions  ... 
doi:10.1101/472217 fatcat:yfbsianlqvb23bu7kz6ifolrlq

Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology

Muhammad Asif, Hugo F. M. C. M. Martiniano, Astrid M. Vicente, Francisco M. Couto, Jianjun Hu
2018 PLoS ONE  
A quantitative measure of gene functional similarities was obtained by employing different semantic similarity measures.  ...  a quantitative measure of gene functional similarities.  ...  Acknowledgments We would like to thank Ana Rita Marques and André Lamúrias for their valuable suggestions to improve this work. Author Contributions  ... 
doi:10.1371/journal.pone.0208626 pmid:30532199 pmcid:PMC6287949 fatcat:4fzbiv65fnallcz43dbv4ixyxq

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation

Liat Perlman, Assaf Gottlieb, Nir Atias, Eytan Ruppin, Roded Sharan
2011 Journal of Computational Biology  
We apply our framework to predict targets for hundreds of drugs using both commonly used and novel drug-drug and gene-gene similarity measures and compare our results to existing state of the art methods  ...  The framework consists of a new scoring scheme for drug-gene associations based on a given pair of drug-drug and gene-gene similarity measures, combined with a logistic regression component that integrates  ...  Several approaches, concentrating mainly on indirect drug-gene associations, employed additional similarity measures to gain insights on drugs.  ... 
doi:10.1089/cmb.2010.0213 pmid:21314453 fatcat:um4ovmryynaermnq7e4xgpxfai

A computational framework for the prioritization of disease-gene candidates

Fiona Browne, Haiying Wang, Huiru Zheng
2015 BMC Genomics  
An important challenge now is to identify meaningful disease-associated genes from a long list of candidate genes implicated by these analyses.  ...  Diverse heterogeneous data including: gene-expression, protein-protein interaction network, ontology-based similarity and topological measures and tissue-specific are integrated.  ...  Results and discussion Using an integrative approach defined in the Method section, diverse heteregenous data obtained from AD gene expression, network topological analysis, along with semantic similarity  ... 
doi:10.1186/1471-2164-16-s9-s2 pmid:26330267 pmcid:PMC4547404 fatcat:lsrmroepg5gvrnv4jnmel4ux7a

An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods

Giorgio Valentini, Alberto Paccanaro, Horacio Caniza, Alfonso E. Romero, Matteo Re
2014 Artificial Intelligence in Medicine  
In this paper we aim at providing an extensive analysis of gene-disease associations not limited to genetic disorders, and a a systematic comparison of different network integration methods for gene prioritization  ...  Several works proposed to integrate multiple sources of data to improve disease gene prioritization, but to our knowledge no systematic studies focused on the quantitative evaluation of the impact of network  ...  Acknowledgments We would like to thank the reviewers and the editor for their comments and suggestions.  ... 
doi:10.1016/j.artmed.2014.03.003 pmid:24726035 pmcid:PMC4070077 fatcat:gonqvuf3sray7hsrey7idewbuq

Gene2DisCo: Gene to disease using disease commonalities

Marco Frasca
2017 Artificial Intelligence in Medicine  
Finding the human genes co-causing complex diseases,  ...  Providing novel putative gene-disease associations This section is dedicated to provide predictions for novel candidate genedisease associations.  ...  measures to compute semantic similarity among diseases.  ... 
doi:10.1016/j.artmed.2017.08.001 pmid:28882544 fatcat:m7xxjaqojvcoje6ppndqfd44lm

A multi-network integration approach for measuring disease similarity based on ncRNA regulation and heterogeneous information

Ningyi Zhang, Tianyi Zang
2022 BMC Bioinformatics  
It has been consentaneous that functional associations between disease-related genes and semantic associations can be applied to calculate disease similarity.  ...  Results In this article, we proposed a novel method, ImpAESim, a framework integrating multiple networks embedding to learn compact feature representations and disease similarity calculation.  ...  Studying the relationships can make contributions to predict disease causing genes [3, 4] , inferring miRNA function associations [5, 6] , and identifying novel therapeutic drugs for diseases [7, 8]  ... 
doi:10.1186/s12859-022-04613-1 pmid:35255810 pmcid:PMC8902705 fatcat:a4f2knjwrfakngmhcfb5nml3ki

Network-based collaborative filtering recommendation model for inferring novel disease-related miRNAs

Changlong Gu, Bo Liao, Xiaoying Li, Lijun Cai, Haowen Chen, Keqin Li, Jialiang Yang
2017 RSC Advances  
According to the miRNA and disease similarity network, the unknown associations are predicted by combining the known miRNA-disease association network based on collaborative filtering recommendation algorithm  ...  By integrating disease-gene associations, miRNA-mRNA interactions, and protein-protein interactions, Shi et al. 22 developed an improved method based on RWR to predict disease-related miRNAs and achieved  ...  Based on the common assumption that two diseases with similar functions are normally associated with similar target genes, we also used the NMI of two disease-target gene sets to measure their functional  ... 
doi:10.1039/c7ra09229f fatcat:znmt24lhkjb2nnqklmyshgywcq

How to build personalized multi-omics comorbidity profiles

Mohammad Ali Moni, Pietro Liò
2015 Frontiers in Cell and Developmental Biology  
The functions of POGO offer flexibility for diagnostic applications to predict disease comorbidities, and can be easily integrated to high-throughput and clinical data analysis pipelines.  ...  Moreover, integrated omics and clinical information may potentially improve prediction accuracy of disease comorbidities.  ...  We implemented a semantic similarity measurement to quantify the association between gene ontology and their associated diseases.  ... 
doi:10.3389/fcell.2015.00028 pmid:26157799 pmcid:PMC4478898 fatcat:i4si7dvtdvagjd4lytuyxosnze

MultiSourcDSim: an integrated approach for exploring disease similarity

Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang
2019 BMC Medical Informatics and Decision Making  
This might further imply treatment that can be appropriated from one disease to another. During the past decades, a number of approaches for calculating disease similarity have been developed.  ...  A collection of disease-associated data contributes to study the association between diseases.  ...  The performance of MultiSourcDSim is further evaluated by comparing it with other three recent approaches: the text-based approach, namely MimMiner [34] , an integrated semantic and functional approach  ... 
doi:10.1186/s12911-019-0968-8 pmid:31856813 pmcid:PMC6921439 fatcat:r6etqnn2cfcr5lphb3fiueb3be
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