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Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning
Extracting the drivers from genes with mutation, and segregation of driver and passenger genes are known as the most controversial issues in cancer studies. According to the heterogeneity of cancer, it is not possible to identify indicators under a group of associated drivers, in order to identify a...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080706/ https://www.ncbi.nlm.nih.gov/pubmed/33911156 http://dx.doi.org/10.1038/s41598-021-88548-2 |
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author | Ebadi, Ali Reza Soleimani, Ali Ghaderzadeh, Abdulbaghi |
author_facet | Ebadi, Ali Reza Soleimani, Ali Ghaderzadeh, Abdulbaghi |
author_sort | Ebadi, Ali Reza |
collection | PubMed |
description | Extracting the drivers from genes with mutation, and segregation of driver and passenger genes are known as the most controversial issues in cancer studies. According to the heterogeneity of cancer, it is not possible to identify indicators under a group of associated drivers, in order to identify a group of patients with diseases related to these subgroups. Therefore, the precise identification of the related driver genes using artificial intelligence techniques is still considered as a challenge for researchers. In this research, a new method has been developed using the subspace learning method, unsupervised learning, and with more constraints. Accordingly, it has been attempted to extract the driver genes with more precision and accurate results. The obtained results show that the proposed method is more to predict the driver genes and subgroups of driver genes which have the highest degree of overlap due to p-value with known driver genes in valid databases. Driver genes are the benchmark of MsigDB which have more overlap compared to them as selected driver genes. In this article, in addition to including the driver genes defined in previous work, introduce newer driver genes. The minister will define newer groups of driver genes compared to other methods the p-value of the proposed method was 9.21e-7 better than previous methods for 200 genes. Due to the overlap and newer driver genes and driver gene group and subgroups. The results show that the p value of the proposed method is about 2.7 times less than the driver sub method due to overlap, indicating that the proposed method can identify driver genes in cancerous tumors with greater accuracy and reliability. |
format | Online Article Text |
id | pubmed-8080706 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-80807062021-04-30 Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning Ebadi, Ali Reza Soleimani, Ali Ghaderzadeh, Abdulbaghi Sci Rep Article Extracting the drivers from genes with mutation, and segregation of driver and passenger genes are known as the most controversial issues in cancer studies. According to the heterogeneity of cancer, it is not possible to identify indicators under a group of associated drivers, in order to identify a group of patients with diseases related to these subgroups. Therefore, the precise identification of the related driver genes using artificial intelligence techniques is still considered as a challenge for researchers. In this research, a new method has been developed using the subspace learning method, unsupervised learning, and with more constraints. Accordingly, it has been attempted to extract the driver genes with more precision and accurate results. The obtained results show that the proposed method is more to predict the driver genes and subgroups of driver genes which have the highest degree of overlap due to p-value with known driver genes in valid databases. Driver genes are the benchmark of MsigDB which have more overlap compared to them as selected driver genes. In this article, in addition to including the driver genes defined in previous work, introduce newer driver genes. The minister will define newer groups of driver genes compared to other methods the p-value of the proposed method was 9.21e-7 better than previous methods for 200 genes. Due to the overlap and newer driver genes and driver gene group and subgroups. The results show that the p value of the proposed method is about 2.7 times less than the driver sub method due to overlap, indicating that the proposed method can identify driver genes in cancerous tumors with greater accuracy and reliability. Nature Publishing Group UK 2021-04-28 /pmc/articles/PMC8080706/ /pubmed/33911156 http://dx.doi.org/10.1038/s41598-021-88548-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Ebadi, Ali Reza Soleimani, Ali Ghaderzadeh, Abdulbaghi Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning |
title | Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning |
title_full | Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning |
title_fullStr | Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning |
title_full_unstemmed | Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning |
title_short | Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning |
title_sort | providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080706/ https://www.ncbi.nlm.nih.gov/pubmed/33911156 http://dx.doi.org/10.1038/s41598-021-88548-2 |
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