Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article G-S a Prior Biological Knowledge-Based Pattern Detection and Enrichment Framework for Multi-Omics Data Integration(MDPI, 2025-11-29) Unlu Yazici, Miray; Bakir-Gungor, Burcu; Yousef, MalikThe rapid advancements in high-throughput technologies have led to a dramatic increase in diverse -omics data types, enabling comprehensive analyses, especially for complex diseases like cancer. Despite the development of multi-omics approaches, the challenges of scaling integration to massive, heterogeneous -omics datasets suggest that novel computational tools need to be designed. In this study, we propose an approach for integrating microRNA (miRNA) and messenger RNA (mRNA) expression data, incorporating prior biological knowledge (PBK). This approach scores and ranks groups of miRNAs and their associated genes using cross-validation iterations. The proposed method incorporates a Pattern detection (P) component to identify molecular motifs unique to each biological group. The analysis also facilitates the visualization of the groups, facilitating the identification of co-occurring groups and their characteristic features across iterations. Furthermore, the groups are scored using an over-representation analysis through a new Enrichment (E) component in each iteration. The clusters of the groups based on the Enrichment Scores (ESs) are visualized in a heatmap to obtain novel insights into the collective behavior and dependencies of the groups, aiming to understand the molecular mechanisms of complex diseases. The developed G-S-M-E tool not only provides performance metrics and biological scores at the group level but also offers comprehensive insights into intricate multi-omics interactions. In summary, our study emphasizes the importance of mathematical and data science methodologies in elucidating intricate multi-omics integration, yielding a formalized approach that deepens our comprehension of complex diseases.Article Citation - WoS: 16Citation - Scopus: 20Invention of 3Mint for Feature Grouping and Scoring in Multi-Omics(Frontiers Media S.A., 2023-03-15) Yazici, Miray Unlu; Marron, J. S.; Bakir-Gungor, Burcu; Zou, Fei; Yousef, Malik; Unlu Yazici, MirayAdvanced genomic and molecular profiling technologies accelerated the enlightenment of the regulatory mechanisms behind cancer development and progression, and the targeted therapies in patients. Along this line, intense studies with immense amounts of biological information have boosted the discovery of molecular biomarkers. Cancer is one of the leading causes of death around the world in recent years. Elucidation of genomic and epigenetic factors in Breast Cancer (BRCA) can provide a roadmap to uncover the disease mechanisms. Accordingly, unraveling the possible systematic connections between-omics data types and their contribution to BRCA tumor progression is crucial. In this study, we have developed a novel machine learning (ML) based integrative approach for multi-omics data analysis. This integrative approach combines information from gene expression (mRNA), MicroRNA (miRNA) and methylation data. Due to the complexity of cancer, this integrated data is expected to improve the prediction, diagnosis and treatment of disease through patterns only available from the 3-way interactions between these 3-omics datasets. In addition, the proposed method bridges the interpretation gap between the disease mechanisms that drive onset and progression. Our fundamental contribution is the 3 Multi-omics integrative tool (3Mint). This tool aims to perform grouping and scoring of groups using biological knowledge. Another major goal is improved gene selection via detection of novel groups of cross-omics biomarkers. Performance of 3Mint is assessed using different metrics. Our computational performance evaluations showed that the 3Mint classifies the BRCA molecular subtypes with lower number of genes when compared to the miRcorrNet tool which uses miRNA and mRNA gene expression profiles in terms of similar performance metrics (95% Accuracy). The incorporation of methylation data in 3Mint yields a much more focused analysis. The 3Mint tool and all other supplementary files are available at .