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Prediction of key pathways in hepatocellular carcinoma (HCC): A machine learning approach using a sample pathway information matrix

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Computational Biology and Chemistry 2025年 118卷 108481页

作者： Annadurai, Priyadharshini Isaac, Arnold Emerson Bioinformatics Programming Laboratory Department of Bioscience School of Bio Science and Technology Vellore Institute of Technology Katpadi Tamil Nadu Vellore632014 India

Hepatocellular carcinoma (HCC) represents the most prevalent form of primary liver cancer, accounting for 75 % of all cases. Individuals with metabolic dysfunctions are at risk of developing significant symptoms, including cirrhosis. To address this, we proposed a novel method to find the signalling pathway based on the patient's gene expression. The objective includes examining the predictive biomarkers associated with cirrhosis-related HCC. The study combines gene expression and pathway enrichment data to find the biologically important pathways in disease progression. The differential gene expression analysis showed 58 upregulated and 62 downregulating differentially expressed genes. These DEGs were utilized to construct a protein-protein interaction network, and then the clustered genes were determined. Subsequently, pathway enrichment analysis was performed for the clustered genes and the gene-pathway interaction matrix was developed. The sample-pathway information matrix (SPIM) was obtained by multiplying the gene-expression and gene-pathway matrix. The key pathways were predicted from the SPIM using random forest model and we achieved 94 % of accuracy. The arachidonic acid metabolism was the most important pathway and genes involved in this pathway includes CYP2C9, CYP2C8, CYP2B6. These genes are well known for promoting metabolic disorders in the liver. Hence, our novel method proves that it could distinguish the samples and extract important pathways that are involved in differentiating the diseased samples based on the gene expression. Therefore, integrating gene expression and their enriched biological pathways may effectively help in identifying the key signalling pathways. © 2025 Elsevier Ltd

关键词： Transcription

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Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development

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Developmental Cell 2025年

作者： Chakraborty, Shreeta Wenzlitschke, Nina Anderson, Matthew J. Eraso, Ariel Baudic, Manon Thompson, Joyce J. Evans, Alicia A. Shatford-Adams, Lilly M. Chari, Raj Awasthi, Parirokh Dale, Ryan K. Lewandoski, Mark Petros, Timothy J. Rocha, Pedro P. Unit on Genome Structure and Regulation National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States Genetics of Vertebrate Development Section Cancer and Developmental Biology Laboratory National Cancer Institute National Institutes of Health Frederick 21702 MD United States Bioinformatics and Scientific Programming Core National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States Laboratory Animal Sciences Program Frederick National Laboratory for Cancer Research Frederick 21702 MD United States Unit on Cellular and Molecular Neurodevelopment National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States National Cancer Institute NIH Bethesda 20892 MD United States

Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysregulation and phenotypes. We tested whether perturbing a domain with multiple developmental regulators would lead to more severe outcomes. We chose a domain with three FGF ligand genes—Fgf3, Fgf4, and Fgf15—that control different murine developmental processes. Heterozygous deletion of a 23.9-kb boundary defined by four CTCF sites led to ectopic interactions of the FGF genes with enhancers active in the brain and induced FGF expression. This caused orofacial clefts, encephalocele, and fully penetrant perinatal lethality. Loss of the single CTCF motif oriented toward the enhancers—but not the three toward the FGF genes—recapitulated these phenotypes. Our works shows that small sequence variants at particular domain boundaries can have a surprisingly outsized effect and must be considered as potential sources of gene dysregulation in development and disease. © 2025

关键词： CTCF epigenetics FGF gene regulation nuclear organization

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Interactive workflows in a virtual laboratory for e-bioscience: The SigWin-detector tool for gene expression analysis

Interactive workflows in a virtual laboratory for e-bioscien...

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e-Science 2006 - 2nd IEEE International Conference on e-Science and Grid Computing

作者： Inda, Márcia A. Belloum, Adam S.Z. Roos, Marco Vasunin, Dmitry De Laat, Cees Hertzberger, L.O. Breit, Timo M. Integrative Bioinformatics Unit Faculty of Science University of Amsterdam Netherlands System Network and Engineering Group Faculty of Science University of Amsterdam Netherlands Computer Architecture and Programming Laboratory Group Faculty of Science University of Amsterdam Netherlands

ISBN: (纸本)0769527345

Explorative research is a vital part of biological sciences. Biologists frequently have to examine and compare multiple (large) sets of biological data in an interactive and explorative manner. Exploring alternative ways of examining the data and managing the necessary resources often require substantial (manual) effort and time. In this paper, we present a concrete example of how VLAM, a grid-based workflow management system, can enhance experimentation. We discuss in detail the process of developing the SigWin-detector, an application in the domain of bioinformatics. We show that SigWin-detector can promptly identify regions of increased gene expression in transcriptome maps and periodicity in weather data. We also show that the workflow can be extended or partially modified. The individual modules can also be used to compose different experiments. SigWin-detector fulfills the requirements of interactive and explorative experimentation. ©2006 IEEE.

关键词： Virtual reality

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Author Correction: Anchoring cortical granules in the cortex ensures trafficking to the plasma membrane for post-fertilization exocytosis

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Nature communications 2019年第1期10卷 2926页

作者： Edgar-John Vogt Keizo Tokuhiro Min Guo Ryan Dale Guanghui Yang Seung-Wook Shin Maria Jimenez Movilla Hari Shroff Jurrien Dean Laboratory of Cellular and Developmental Biology NIDDK National Institutes of Health Bethesda MD 20892 USA. Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany. Department of Genome Editing Institute of Biomedical Science Kansai Medical University 2-5-1 Shinmachi Hirakata Osaka 573-1010 Japan. Section on High Resolution Optical Imaging NIBIB National Institutes of Health Bethesda MD 20892 USA. Bioinformatics and Scientific Programming Core Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD 20892 USA. Department of Cell Biology and Histology Medical School University of Murcia IMIB 30100 Murcia Spain. Advanced Imaging and Microscopy Resource National Institutes of Health Bethesda MD 20892 USA. Laboratory of Cellular and Developmental Biology NIDDK National Institutes of Health Bethesda MD 20892 USA. jurrien.dean@nih.gov.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

关键词： Actin Exocytosis Super-resolution microscopy

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