A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease Modules
Traditional techniques for identifying disease genes and disease modules involve high-cost clinical experiments and unpredictable time consumption for analysis. Network-based computational approaches usually focus on the systematic study of molecular networks to predict the associations between dise...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
IEEE
2023-01-01
|
| Series: | IEEE Access |
| Subjects: | |
| Online Access: | https://ieeexplore.ieee.org/document/10286485/ |
| _version_ | 1797649763436331008 |
|---|---|
| author | Tay Xin Hui Shahreen Kasim Mohd Farhan Md. Fudzee Tole Sutikno Rohayanti Hassan Izzatdin Abdul Aziz Mohd Hilmi Hasan Jafreezal Jaafar Metab Alharbi Seah Choon Sen |
| author_facet | Tay Xin Hui Shahreen Kasim Mohd Farhan Md. Fudzee Tole Sutikno Rohayanti Hassan Izzatdin Abdul Aziz Mohd Hilmi Hasan Jafreezal Jaafar Metab Alharbi Seah Choon Sen |
| author_sort | Tay Xin Hui |
| collection | DOAJ |
| description | Traditional techniques for identifying disease genes and disease modules involve high-cost clinical experiments and unpredictable time consumption for analysis. Network-based computational approaches usually focus on the systematic study of molecular networks to predict the associations between diseases and genes. The random walk-based method is a network-based approach that utilises biological networks for analysis. As the random walk models efficiently capture the complex interplay among molecules in diseases, it is extensively applied in biological problem-solving based on networks. Despite their comprehensive employment, the fundamentals of random walk and overall background may not be fully understood, leading to misinterpretation of results. This review aims to cover the fundamental knowledge of random walk models for biological network analysis. This study reviewed diffusion-based random walk methods for disease gene prediction and disease module identification. The random walk-based disease gene prediction methods are categorised into node classification and link prediction tasks. This study details the advantages and limitations of each method. Finally, the potential challenges and research directions for future studies on random walk models are highlighted. |
| first_indexed | 2024-03-11T15:50:42Z |
| format | Article |
| id | doaj.art-29184bc0b83e480493105c908925d81c |
| institution | Directory Open Access Journal |
| issn | 2169-3536 |
| language | English |
| last_indexed | 2024-03-11T15:50:42Z |
| publishDate | 2023-01-01 |
| publisher | IEEE |
| record_format | Article |
| series | IEEE Access |
| spelling | doaj.art-29184bc0b83e480493105c908925d81c2023-10-25T23:00:59ZengIEEEIEEE Access2169-35362023-01-011111636611638310.1109/ACCESS.2023.332498510286485A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease ModulesTay Xin Hui0https://orcid.org/0009-0007-0016-7555Shahreen Kasim1Mohd Farhan Md. Fudzee2https://orcid.org/0000-0002-6801-2660Tole Sutikno3https://orcid.org/0000-0002-1595-2915Rohayanti Hassan4Izzatdin Abdul Aziz5https://orcid.org/0000-0003-2654-4463Mohd Hilmi Hasan6Jafreezal Jaafar7https://orcid.org/0000-0002-8850-6203Metab Alharbi8Seah Choon Sen9https://orcid.org/0000-0003-0328-7505Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Parit Raja, MalaysiaFaculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Parit Raja, MalaysiaFaculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Parit Raja, MalaysiaDepartment of Electrical Engineering, Universitas Ahmad Dahlan (UAD), Yogyakarta, IndonesiaFaculty of Electrical Engineering, Universiti Teknologi Malaysia (UTM), Skudai, MalaysiaComputer and Information Sciences Department (CISD), Universiti Teknologi PETRONAS (UTP), Seri Iskandar, Perak, MalaysiaComputer and Information Sciences Department (CISD), Universiti Teknologi PETRONAS (UTP), Seri Iskandar, Perak, MalaysiaComputer and Information Sciences Department (CISD), Universiti Teknologi PETRONAS (UTP), Seri Iskandar, Perak, MalaysiaDepartment of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaFaculty of Accounting and Management, Universiti Tunku Abdul Rahman (UTAR), Kajang, MalaysiaTraditional techniques for identifying disease genes and disease modules involve high-cost clinical experiments and unpredictable time consumption for analysis. Network-based computational approaches usually focus on the systematic study of molecular networks to predict the associations between diseases and genes. The random walk-based method is a network-based approach that utilises biological networks for analysis. As the random walk models efficiently capture the complex interplay among molecules in diseases, it is extensively applied in biological problem-solving based on networks. Despite their comprehensive employment, the fundamentals of random walk and overall background may not be fully understood, leading to misinterpretation of results. This review aims to cover the fundamental knowledge of random walk models for biological network analysis. This study reviewed diffusion-based random walk methods for disease gene prediction and disease module identification. The random walk-based disease gene prediction methods are categorised into node classification and link prediction tasks. This study details the advantages and limitations of each method. Finally, the potential challenges and research directions for future studies on random walk models are highlighted.https://ieeexplore.ieee.org/document/10286485/Random walkdisease gene predictiondisease module identificationdisease-gene prioritisationbiological network |
| spellingShingle | Tay Xin Hui Shahreen Kasim Mohd Farhan Md. Fudzee Tole Sutikno Rohayanti Hassan Izzatdin Abdul Aziz Mohd Hilmi Hasan Jafreezal Jaafar Metab Alharbi Seah Choon Sen A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease Modules IEEE Access Random walk disease gene prediction disease module identification disease-gene prioritisation biological network |
| title | A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease Modules |
| title_full | A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease Modules |
| title_fullStr | A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease Modules |
| title_full_unstemmed | A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease Modules |
| title_short | A Review of Random Walk-Based Method for the Identification of Disease Genes and Disease Modules |
| title_sort | review of random walk based method for the identification of disease genes and disease modules |
| topic | Random walk disease gene prediction disease module identification disease-gene prioritisation biological network |
| url | https://ieeexplore.ieee.org/document/10286485/ |
| work_keys_str_mv | AT tayxinhui areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT shahreenkasim areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT mohdfarhanmdfudzee areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT tolesutikno areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT rohayantihassan areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT izzatdinabdulaziz areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT mohdhilmihasan areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT jafreezaljaafar areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT metabalharbi areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT seahchoonsen areviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT tayxinhui reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT shahreenkasim reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT mohdfarhanmdfudzee reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT tolesutikno reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT rohayantihassan reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT izzatdinabdulaziz reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT mohdhilmihasan reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT jafreezaljaafar reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT metabalharbi reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules AT seahchoonsen reviewofrandomwalkbasedmethodfortheidentificationofdiseasegenesanddiseasemodules |