Gene Expression High-Dimensional Clustering towards a Novel, Robust, Clinically Relevant and Highly Compact Cancer Signature

Abstract : Precision medicine, a highly disruptive paradigm shift in healthcare targeting the personalizing treatment, heavily relies on genomic data. However, the complexity of the biological interactions, the important number of genes as well as the lack of substantial patient's clinical data consist a tremendous bottleneck on the clinical implementation of precision medicine. In this work, we introduce a generic, low dimensional gene signature that represents adequately the tumor type. Our gene signature is produced using LP-stability algorithm, a high dimensional center-based unsupervised clustering algorithm working in the dual domain, and is very versatile as it can consider any arbitrary distance metric between genes. The gene signature produced by LP-stability reports at least $10$ times better statistical significance and $35\%$ better biological significance than the ones produced by two referential unsupervised clustering methods. Moreover, our experiments demonstrate that our low dimensional biomarker ($27$ genes) surpass significantly existing state of the art methods both in terms of qualitative and quantitative assessment while providing better associations to tumor types than methods widely used in the literature that rely on several omics data.
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https://hal.archives-ouvertes.fr/hal-02076104
Contributor : Enzo Battistella <>
Submitted on : Thursday, March 21, 2019 - 9:10:38 PM
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Enzo Battistella, Maria Vakalopoulou, Théo Estienne, Marvin Lerousseau, Roger Sun, et al.. Gene Expression High-Dimensional Clustering towards a Novel, Robust, Clinically Relevant and Highly Compact Cancer Signature. IWBBIO 2019 - 7th International Work-Conference on Bioinformatics and Biomedical Engineering, May 2019, Granada, Spain. ⟨hal-02076104⟩

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