Pathway-based Deep Clustering for Molecular Subtyping of Cancer

Publication date: Available online 25 June 2019Source: MethodsAuthor(s): Tejaswini Mallavarapu, Jie Hao, Youngsoon Kim, Jung Hun Oh, Mingon KangAbstractCancer is a genetic disease comprising multiple subtypes that have distinct molecular characteristics and clinical features. Cancer subtyping helps in improving personalized treatment and making decision, as different cancer subtypes respond differently to the treatment. The increasing availability of cancer related genomic data provides the opportunity to identify molecular subtypes. Several unsupervised machine learning techniques have been applied on molecular data of the tumor samples to identify cancer subtypes that are genetically and clinically distinct. However, most clustering methods often fail to efficiently cluster patients due to the challenges imposed by high-throughput genomic data and its non-linearity. In this paper, we propose a pathway-based deep clustering method (PACL) for molecular subtyping of cancer, which incorporates gene expression and biological pathway database to group patients into cancer subtypes. The main contribution of our model is to discover high-level representations of biological data by learning complex hierarchical and nonlinear effects of pathways. We compared the performance of our model with a number of benchmark clustering methods that recently have been proposed in cancer subtypes. We assessed the hypothesis that clusters (subtypes) may be associated to different survivals by logra...
Source: Methods - Category: Molecular Biology Source Type: research

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Source: Nanomedicine: Nanotechnology, Biology and Medicine - Category: Nanotechnology Source Type: research
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Source: Biosensors and Bioelectronics - Category: Biotechnology Source Type: research
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Source: Journal of Molecular Structure - Category: Molecular Biology Source Type: research
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Source: RSC - Soft Matter latest articles - Category: Chemistry Authors: Source Type: research
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Source: SafetyLit - Category: International Medicine & Public Health Tags: Suicide and Self-Harm Source Type: news
Fentanyl is a potent synthetic opioid with a variety of possible applications. Transdermal fentanyl patches are regularly prescribed for patients with severe chronic or cancer-related pain. The potential for abuse is well-known and cases associated with il...
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Shareholders have approved a plan making Flex Pharma, the neurobiology-focused biotech started five years ago by a Nobel Prize winner and one of the founders of Alnylam Pharmaceuticals Inc., into a shell company for a privately held Houston cancer drug developer.   Flex Pharma (Nasdaq: FLKS) was co-founded in 2014 by Nobel Prize Winner Rod MacKinnon and serial entrepreneur Christoph Westphal. The company began looking for a merger partner after its “tolerability concerns” arose during a mid-stage…
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Cancer cells depend on lengthening their telomeres, usually via telomerase activity. Telomeres are the caps of repeated DNA sequences at the ends of chromosomes. A little length is lost with each cell division, and when short a cell either self-destructs or becomes senescent and ceases replication. Cancer cells can only replicate continually if telomeres are extended continually. Thus some research groups are looking into sabotage of telomerase or the alternative lengthening of telomeres (ALT) processes as the basis for a truly universal cancer therapy. Others, as here, are investigating ways to interfere in mechanisms tha...
Source: Fight Aging! - Category: Research Authors: Tags: Daily News Source Type: blogs
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Source: HSJ - Category: UK Health Source Type: news
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