Integrated analysis identifies oxidative stress-related lncRNAs associated with progression and prognosis in colorectal cancer

Figures

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  Fig. 1. Volcano plot of DEOSGs between CRC and normal samples. Dots in green represent significantly downregulated genes, dots in red represent significantly upregulated genes, and dots in gray represent genes whose expression levels were not changed significantly

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  Fig. 2. KEGG enrichment analysis of DEOSGs [20–22]. A, B Top 30 classes of KEGG enrichment terms. Cluster diagram (C) and Circle diagram (D) showing terms enriched in KEGG analysis

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  Fig. 3. GO enrichment analysis of the DEOSGs. A, B Top 10 classes of GO enrichment terms in the biological process (BP), cellular component (CC), and molecular function (MF) categories. Cluster diagram (C) and circle diagram (D) showing terms enriched in GO analysis

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  Fig. 4. Construction of a prognostic model. A, B LASSO analysis for determining the number of factors and constructing the prognosis prediction model. C Survival curve. D, E Risk score distribution and survival status F heatmap showing the expression levels of the 9 lncRNAs in patients in the low- and high-risk groups. G TimeROC curves for forecasting OS

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  Fig. 5. A The lncRNA–mRNA network between nine oxidative stress-associated lncRNAs and relevant mRNAs. Green circles indicate oxidative stress-associated lncRNAs. Red squares indicate mRNAs. The line represents a coexpression relationship between the lncRNA and the mRNA. B A Sankey diagram showed the co-occurrences of lncRNAs, mRNAs, and characteristics according to the risk score

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  Fig. 6. Efficacy evaluation of the constructed prognostic model. Univariate (A) and multivariate (B) Cox regression analyses of the clinicopathological features. Clinical ROC curves at 1 year (C) and 5 years (D) for forecasting overall survival. The relationship between the risk score and stage I-II (E) and stage III-IV (F). G The constructed C-index curve. H The constructed nomogram of the risk score and other clinical factors for predicting the OS of patients with CRC at 1, 3, and 5 years. I The calibration plot of the nomogram

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  Fig. 7. Evaluation of the efficacy of the constructed prognostic model. PCA of the risk groups in the testing (A) and training sets (B). PCA-3D of the risk groups based on all OS genes (C), DEOSGs (D), and 9 oxidative stress-related lncRNAs (E). The t-SNE of risk groups in the testing (F) and training sets (G)

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  Fig. 8. K-M survival curves for 4 target lncRNAs in CRC. The horizontal coordinate of the KM-plot is the survival time and the vertical coordinate is the survival rate. The starting point is the time of the start of follow-up, the falling curve represents patient death, and the " + "sign on the curve indicates censoring (last follow-up time for patients who are still alive)

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  Fig. 9. TMB analysis. The mutation rates in the high- (A) and low-risk groups (B). C–D Survival analysis of patients with different TMB levels. E Comparison of TMB for patients in the high- and low-risk groups. F Relevance analysis of TMB

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  Fig. 10. TMB analysis in the MSI-positive and MSI-negative groups. Survival analysis of patients with different TMB levels and different risk scores in the MSI-positive (A, B) and MSI-negative groups (C, D). Comparison of TMB in patients with high- and low-risk scores in the MSI-positive (E) and MSI-negative groups (F). Relevance analysis of TMB in the MSI-positive (G) and MSI-negative groups (H)

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  Fig. 11. Investigation of immune cell infiltration and clinical treatment in different risk groups. GSEA of the top 10 pathways significantly enriched in the high-risk group (A) and low-risk group (B). C, D The immune cell heatmap of different risk groups. E The comparison of immune-related scores between the low- and high-risk groups. F The comparison of ratios of infiltrated immune cells between the low- and high-risk groups. G Survival curve of resting NK cells. H The comparison of immune functions between the low- and high-risk groups. I The comparison of immune subtypes between the low- and high-risk groups

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  Fig. 12. Investigation of immune cell infiltration and clinical treatment in different risk groups. A–C The comparison of immune-related scores between the low- and high-risk groups. D The comparison of the response to immunotherapy between the low- and high-risk groups. E‒N The immunotherapy prediction of different risk groups