A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability
We introduce a network-based approach to identify subnets of functionally-related genes for predicting 5-year survivability of breast cancer patients treated with chemotherapy, hormone therapy, and a combination of these. A gene expression dataset and a protein-protein interaction network are integr...
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| Định dạng: | Conference paper |
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2023
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oai:scholar.dlu.edu.vn:123456789-26952023-12-13T03:25:46Z A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability Phạm, Quang Huy Alioune Ngom Luis Rueda Data integration Sub-network selection Sub-network biomarkers Breast cancer biomarkers Survivability prediction Network-based classification We introduce a network-based approach to identify subnets of functionally-related genes for predicting 5-year survivability of breast cancer patients treated with chemotherapy, hormone therapy, and a combination of these. A gene expression dataset and a protein-protein interaction network are integrated to construct a weighted graph, where edge weight expresses the predictability of the two corresponding genes in predicting the class. We propose a scoring criterion to measure the density of a weighted sub-graph, which is also an estimation of its predictive power. Thus, we can identify an optimally-dense sub-network for each seed gene, and then evaluate that sub-network by classification method. Finally, among the sub-networks whose classification performance greater than a given threshold, we search for an optimal set of sub-networks that can further improve classification performance via a voting scheme. We significantly improved the results of existing approaches. For each type of treatment, our best prediction model can reach 85% accuracy or more. Many selected sub-networks used to construct the voting models contain breast/other cancer-related genes including SP1, TP53, MYC, NOG, and many more, providing pieces of evidence for down-stream analysis. 12108 2023-06-14T12:46:08Z 2023-06-14T12:46:08Z 2020 Conference paper Bài báo đăng trên tạp chí quốc tế (có ISSN), bao gồm book chapter https://scholar.dlu.edu.vn/handle/123456789/2695 10.1007/978-3-030-45385-5_5 en Lecture Notes in Computer Science IWBBIO 2020 Springer |
| institution |
Thư viện Trường Đại học Đà Lạt |
| collection |
Thư viện số |
| language |
English |
| topic |
Data integration Sub-network selection Sub-network biomarkers Breast cancer biomarkers Survivability prediction Network-based classification |
| spellingShingle |
Data integration Sub-network selection Sub-network biomarkers Breast cancer biomarkers Survivability prediction Network-based classification Phạm, Quang Huy Alioune Ngom Luis Rueda A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability |
| description |
We introduce a network-based approach to identify subnets of functionally-related genes for predicting 5-year survivability of breast cancer patients treated with chemotherapy, hormone therapy, and a combination of these. A gene expression dataset and a protein-protein interaction network are integrated to construct a weighted graph, where edge weight expresses the predictability of the two corresponding genes in predicting the class. We propose a scoring criterion to measure the density of a weighted sub-graph, which is also an estimation of its predictive power. Thus, we can identify an optimally-dense sub-network for each seed gene, and then evaluate that sub-network by classification method. Finally, among the sub-networks whose classification performance greater than a given threshold, we search for an optimal set of sub-networks that can further improve classification performance via a voting scheme. We significantly improved the results of existing approaches. For each type of treatment, our best prediction model can reach 85% accuracy or more. Many selected sub-networks used to construct the voting models contain breast/other cancer-related genes including SP1, TP53, MYC, NOG, and many more, providing pieces of evidence for down-stream analysis. |
| format |
Conference paper |
| author |
Phạm, Quang Huy Alioune Ngom Luis Rueda |
| author_facet |
Phạm, Quang Huy Alioune Ngom Luis Rueda |
| author_sort |
Phạm, Quang Huy |
| title |
A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability |
| title_short |
A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability |
| title_full |
A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability |
| title_fullStr |
A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability |
| title_full_unstemmed |
A Data Integration Approach for Detecting Biomarkers of Breast Cancer Survivability |
| title_sort |
data integration approach for detecting biomarkers of breast cancer survivability |
| publisher |
Springer |
| publishDate |
2023 |
| url |
https://scholar.dlu.edu.vn/handle/123456789/2695 |
| _version_ |
1785973219887415296 |