Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Citation - WoS: 15Citation - Scopus: 15PriPath: Identifying Dysregulated Pathways From Differential Gene Expression via Grouping, Scoring, and Modeling With an Embedded Feature Selection Approach(BMC, 2023-02-23) Yousef, Malik; Ozdemir, Fatma; Jaber, Amhar; Allmer, Jens; Bakir-Gungor, BurcuBackgroundCell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks can be viewed as modules that provide specific functionality to an organism. The Kyoto encyclopedia of genes and genomes (KEGG) systematically analyzes gene functions, proteins, and molecules and combines them into pathways. Measurements of gene expression (e.g., RNA-seq data) can be mapped to KEGG pathways to determine which modules are affected or dysregulated in the disease. However, genes acting in multiple pathways and other inherent issues complicate such analyses. Many current approaches may only employ gene expression data and need to pay more attention to some of the existing knowledge stored in KEGG pathways for detecting dysregulated pathways. New methods that consider more precompiled information are required for a more holistic association between gene expression and diseases.ResultsPriPath is a novel approach that transfers the generic process of grouping and scoring, followed by modeling to analyze gene expression with KEGG pathways. In PriPath, KEGG pathways are utilized as the grouping function as part of a machine learning algorithm for selecting the most significant KEGG pathways. A machine learning model is trained to differentiate between diseases and controls using those groups. We have tested PriPath on 13 gene expression datasets of various cancers and other diseases. Our proposed approach successfully assigned biologically and clinically relevant KEGG terms to the samples based on the differentially expressed genes. We have comparatively evaluated the performance of PriPath against other tools, which are similar in their merit. For each dataset, we manually confirmed the top results of PriPath in the literature and found that most predictions can be supported by previous experimental research.ConclusionsPriPath can thus aid in determining dysregulated pathways, which applies to medical diagnostics. In the future, we aim to advance this approach so that it can perform patient stratification based on gene expression and identify druggable targets. Thereby, we cover two aspects of precision medicine.Article Citation - WoS: 3Citation - Scopus: 4Investigating the Carbon Border Adjustment Mechanism Transition Process With Linguistic Summarization Method: A Situational Analysis of Exporting Countries(Elsevier Sci Ltd, 2024-08) Fidan, Fatma Sener; Aydogan, Sena; Akay, Diyar; Şener Fidan, FatmaThe Paris Agreement holds significant importance since it establishes a global framework for addressing the issue of climate change and endeavors to mitigate the release of greenhouse gases. The Carbon Border Adjustment Mechanism was introduced as an integral component of this agreement, aiming to oversee the carbon emissions associated with imported items within the European Union and provide compensation for the emissions from the nations engaged in importation. It is essential to analyze the countries involved in exporting to the European Union within the Carbon Border Adjustment Mechanism context to mitigate carbon leakage and effectively support the objectives outlined in the Paris Agreement. This research investigated 104 nations engaged in exporting activities to 27 European Union member countries. The linguistic summarization method, a descriptive data analytics tool, was employed for the analysis. A total of 42 Combined Nomenclature codes were encompassed within the scope of evaluation throughout the transition phase of the Carbon Border Adjustment Mechanism. This study examines the characteristics of exporting nations based on three variables: The Environmental Performance Index, a sustainability indicator; the Region in which the countries are located as classified by the World Bank; and the quantity of Renewable Energy Consumption. Additionally, the study explores the characteristics of EU countries, focusing on their Environmental Performance Index score and geography. The study employed fuzzy sets and the fuzzy c-means algorithm as parts of the linguistic summarization technique. Polyadic quantifiers were used to extract linguistic summaries, resulting in the acquisition of 124,227 summaries. A total of 1594 summaries have a truth degree exceeding 0.9. The findings were effectively utilized to assess the influence of the linguistic summarization approach and offered a valuable viewpoint for decisionmakers needing more expertise in this domain.Article Citation - WoS: 4Citation - Scopus: 4Integrated Querying and Version Control of Context-Specific Biological Networks(Oxford Univ Press, 2020) Cowman, Tyler; Coskun, Mustafa; Grama, Ananth; Koyuturk, MehmetMotivation: Biomolecular data stored in public databases is increasingly specialized to organisms, context/pathology and tissue type, potentially resulting in significant overhead for analyses. These networks are often specializations of generic interaction sets, presenting opportunities for reducing storage and computational cost. Therefore, it is desirable to develop effective compression and storage techniques, along with efficient algorithms and a flexible query interface capable of operating on compressed data structures. Current graph databases offer varying levels of support for network integration. However, these solutions do not provide efficient methods for the storage and querying of versioned networks. Results: We present VerTIoN, a framework consisting of novel data structures and associated query mechanisms for integrated querying of versioned context-specific biological networks. As a use case for our framework, we study network proximity queries in which the user can select and compose a combination of tissue-specific and generic networks. Using our compressed version tree data structure, in conjunction with state-of-the-art numerical techniques, we demonstrate real-time querying of large network databases. Conclusion: Our results show that it is possible to support flexible queries defined on heterogeneous networks composed at query time while drastically reducing response time for multiple simultaneous queries. The flexibility offered by VerTIoN in composing integrated network versions opens significant new avenues for the utilization of ever increasing volume of context-specific network data in a broad range of biomedical applications. Availability and Implementation: VerTIoN is implemented as a C++ library and is available at http://compbio.case.edu/omics/software/vertion and https://github.com/tjcowman/vertion Contact: tyler.cowman@case.edu