دورية أكاديمية
GEGE: Predicting Gene Essentiality with Graph Embeddings
| العنوان: | GEGE: Predicting Gene Essentiality with Graph Embeddings |
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| المؤلفون: | Yasin İlkağan Tepeli, Halil İbrahim Kuru, Öznur Taştan |
| المصدر: | Düzce Üniversitesi Bilim ve Teknoloji Dergisi, Vol 10, Iss 3, Pp 1567-1577 (2022) |
| بيانات النشر: | Düzce University, 2022. |
| سنة النشر: | 2022 |
| المجموعة: | LCC:Technology LCC:Engineering (General). Civil engineering (General) LCC:Science LCC:Science (General) |
| مصطلحات موضوعية: | çizge gösterimleri, düğüm gömülümleri, gen esaslılığı, ağ topolojik özellikleri, protein-protein etkileşim ağı, graph representations, node embeddings, gene essentiality, network topological features, protein-protein interaction network, Technology, Engineering (General). Civil engineering (General), TA1-2040, Science, Science (General), Q1-390 |
| الوصف: | A gene is considered essential if its function is indispensable for the viability or reproductive success of a cell or an organism. Distinguishing essential genes from non-essential ones is a fundamental question in genetics, and it is key to understanding the minimal set of functional requirements of an organism. Knowledge of the set of essential genes is also crucial in drug discovery. Several reports in the literature show that the gene location in a protein-protein interaction network is correlated with the target gene’s essentiality. Here, we ask whether the node embeddings of a protein-protein interaction (PPI) network can help predict gene essentiality. Our results on predicting human gene essentiality show that node embeddings alone can achieve up to 88% AUC score, which is better than using topological features to characterize gene properties and other previous work’s results. We also show that, when combined with homology information across species, this performance reaches 89% AUC. Our work shows that node embeddings of a protein in the PPI network capture the network connectivity patterns of the proteins and improve the gene essentiality predictions. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English Turkish |
| تدمد: | 2148-2446 |
| Relation: | https://dergipark.org.tr/tr/download/article-file/2099646; https://doaj.org/toc/2148-2446 |
| DOI: | 10.29130/dubited.1028387 |
| URL الوصول: | https://doaj.org/article/f71d776e94ea4253b5fe85268c09c291 |
| رقم الأكسشن: | edsdoj.f71d776e94ea4253b5fe85268c09c291 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 21482446 |
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| DOI: | 10.29130/dubited.1028387 |