R software

Univariate and multivariate analyses were evaluated by Cox proportional hazards regression models. The relationship between FTO expression and target genes expression was examined by Spearman correlation test. The OS was plotted by Kaplan-Meier survival analysis. All statistical analyses were calculated by R software (V 4.0.0) and GraphPad Prism 8. P<0.05 was regarded statistically significant.

Statistical analyses and data visualizations were done using GraphPad Prism version 9.0 for Macintosh (GraphPad Software, San Diego, CA) and R software, version 4.1.2 (Vienna, Austria). Statistical significance was assigned when P < 0.05. All data are represented as mean ± standard deviation unless otherwise indicated. Statistical significance of pair-wise comparisons was determined using unpaired Student’s t-tests following Shapiro–Wilk test for normality. For multiple comparisons testing, correlation analysis via Pearson’s chi-squared analysis was performed in combination with linear multiple linear regression, as follows: $$\mathbf{M}\mathbf{a}\mathbf{t}\mathbf{c}\mathbf{h}\mathbf{R}\mathbf{a}\mathbf{n}\mathbf{k}\#={{\mathrm{\beta }}_0+\mathrm{\beta }}_1\left(\mathrm{Step},1\right)+{\mathrm{\beta }}_2\left(\mathrm{Step},2,\mathrm{CK}\right)+{\mathrm{\beta }}_3\left(1^{\mathrm{st}},\mathrm{Author}\right)+{\mathrm{\beta }}_4\left(\mathrm{CoAuthor}\right)+{\mathrm{\beta }}_5\left(\#,\mathrm{Applied}\right)+{\mathrm{\beta }}_6\left(\#,\mathrm{Interiews}\right)$$

Data analysis was performed using R software (GraphPad Software, Inc., La Jolla, CA, USA) and GraphPad Prism (GraphPad Software, Inc., San Diego, CA). To determine statistical significance of differences between two groups, an unpaired t-test was used. For data involving more than two groups, one-way ANOVA was used. A P-value less than 0.05 was considered to indicate statistical significance.

Sequence analysis was performed using Uparse software (Uparse v7.0.1001). Sequences with ≥97% similarity were assigned to the same OTUs. To study the phylogenetic relationships of different OTUs and the differences between the dominant species in different groups, multiple sequence alignment was conducted using MUSCLE software (version 3.8.31). Alpha diversity was applied to analyze the complexity of the species diversity for a sample through three indices, including Chao1, Shannon, and good coverage. All these indices in our samples were calculated with QIIME (version 1.7.0) and visualized with R software (version 2.15.3). The beta diversity based on weighted UniFrac was calculated using QIIME software (version 1.9.1). Random forest analysis evaluates the importance of each predictor by determining how much the mean square error (MSE) increases. The variables were selected when the predictor variables were randomly replaced and the other variables remained unchanged. These analyses were performed using the “RandomForest” package in R. The “Hmisc” package was used to calculate the correlation, the “igraph” package was used to analyses the co-occurrence network (Csardi and Nepusz, 2006 ), and Gephi 0.9.2 software was used to draw the network map. The statistical analyses using the R software and GraphPad Prism.

Statistical analyses were performed using R software (v4.2.2) and GraphPad Prism (v8.0). Survival analyses employed the log-rank test on Kaplan-Meier survival curves to assess the impact of high- and low-expression risk models on patient overall survival (OS). Correlation analysis was conducted using Spearman’s method. The Wilcoxon test was employed to compare scores (TIDE, IPS) between groups. Student’s t-test was conducted to compare results of CCK-8, apoptosis, migration, invasion, cell adhesion, and the ratio of ki-67, IFN-γ, and TNF-α. Data were presented as means ± standard deviation (SD). A significance level of p < .05 was considered statistically significant.

Data analysis was performed by the GraphPad Prism version 8.4.1 for Windows (GraphPad Software, LLC) and the R software (version 4.0.1., R Development Core Team). The level of statistical significance was set at p < 0.05. Non-parametric tests (Kruskall-Walli’s test) were used to compare data expressed in medians between groups. Frequencies of neutralizing antibody titers were compared by chi-square test.