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Biomarkers prediction and immune landscape in ulcerative colitis: Findings based on bioinformatics and machine learning

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机构: [1]Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China [2]The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China [3]State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, [4]Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China [5]Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China [6]Yang Chunbo academic experience inheritance studio of Guangdong provincial hospital of Chinese Medicine, Guangzhou, 510006, China
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关键词: Ulcerative colitis Biomarkers Immune infiltration Bioinformatics Machine learning Deep learning model

摘要:
Ulcerative colitis (UC) presents diagnostic and therapeutic difficulties. The primary objective of this study is to identify efficacious biomarkers for diagnosis and treatment, as well as acquire a deeper understanding of the immuneological characteristics associated with the disease.Datasets relating to UC were obtained from GEO database. Among these, three datasets were merged to create a metadata for bioinformatics analysis and machine learning. Additionally, one dataset specifically utilized for external validation. Least absolute shrinkage and selection operator (LASSO) and random forest (RF) were employed to screen signature genes. The artificial neural network (ANN) model and receiver operating characteristic (ROC) curve were used to assess the diagnostic performance of signature genes. The single sample gene set enrichment analysis (ssGSEA) was applied to reveal the immune landscape. Finally, the relationship between the signature genes, immune infiltration, and clinical characteristics was investigated through correlation analysis.By intersecting the result of LASSO, RF and WGCNA, 8 signature genes were identified, including S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14. The biological progress of this gene mostly encompasses acute inflammatory response, aggregation and chemotaxis of leukocyte, and response to lipopolysaccharide by mediating IL-17 signaling pathway, NF-kappa B signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway. Immune infiltration analysis shows 25 immune cells are significantly elevated in UC samples. Moreover, these signature genes exhibit a strong correlation with various immune cells and a mild to moderate correlation with the Mayo score.S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14 have been identified as credible potential biomarkers for the diagnosis and therapy of UC. The immune response mediated by these signature biomarkers plays a crucial role in the occurrence and advancement of UC by means of the reciprocal interaction between the signature biomarkers and immune-infiltrated cells.Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.

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出版当年[2023]版:
大类 | 2 区 医学
小类 | 1 区 生物学 1 区 数学与计算生物学 2 区 计算机:跨学科应用 2 区 工程:生物医学
最新[2025]版:
大类 | 2 区 医学
小类 | 1 区 数学与计算生物学 2 区 生物学 2 区 计算机:跨学科应用 2 区 工程:生物医学
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出版当年[2022]版:
Q1 BIOLOGY Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Q1 ENGINEERING, BIOMEDICAL Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY
最新[2023]版:
Q1 BIOLOGY Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Q1 ENGINEERING, BIOMEDICAL Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY

影响因子: 最新[2023版] 最新五年平均 出版当年[2022版] 出版当年五年平均 出版前一年[2021版] 出版后一年[2023版]

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第一作者机构: [1]Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
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通讯机构: [1]Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China [2]The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China [3]State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, [4]Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China [5]Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China [6]Yang Chunbo academic experience inheritance studio of Guangdong provincial hospital of Chinese Medicine, Guangzhou, 510006, China [*1]State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
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