一般我们认为NES绝对值≧ 1.0，NOM p-val ≦ 0.05，FDR q-val ≦ 0.25是有意义的基因集合，当然也要结合具体情况具体分析

    Statistical Analysis
    The statistics were executed in the R software (Version 4.1.1). A P-value of less than 0.05 was taken as statistically signifificant for all the analyses. Spearman correlation analysis was used to evaluate the correlation between continuous variables. Variables between two groups were compared by Mann Whitney U test (Wilcoxon rank sum test).

    Use R software (version 4.1.1) to perform statistics. Consider P-values less than 0.05 as statistically significant for all analyses. Spearman correlation analysis is used to assess the correlation between continuous variables. The Mann Whitney U test (Wilcoxon rank sum test) was used to compare the variables between the two groups.

    All statistics were executed in the R software (Version 4.1.1). A P-value of less than 0.05 was taken as statistically signifificant for all the analyses.

    Associations between LDH, SCC, TGSF, CA199 and immune cells were determined using spearman correlation coeffificient.

    The immune cells and their comparisons between NPD and PD and at dignosis and NPD patients were analyzed using Mann-Whitney U test(Wilcoxon rank sum test，paired and two sided).
    Other comparisons of values between two groups groups were performed using Mann-Whitney U tests (Wilcoxon rank sum test).

    The Mann–Whitney U test was used to determine statistical difference between two groups, and the Kruskal–Wallis test was used to determine statistical difference among three groups. Paired samples were compared using Wilcoxon matched-pairs signed-rank test.
    Spearman’s rank coefficient was used to determine correlations, and nonlinear regression (least squares ordinary fit) was also applied when plotted. Overall survival (OS) time and event-free survival (EFS) time were calculated for survival analyses, and median values were used for grouping the patients. The Kaplan–Meier log-rank test was used to compare between-group survival differences.

    The statistics were executed in the R software (Version 4.1.1). The Mann–Whitney U test (Wilcoxon rank sum test) was used to determine statistical difference between two groups. Paired samples were compared using Wilcoxon matched-pairs signed-rank test.
    Spearman correlation analysis was used to evaluate the correlation between continuous variables, and linear regression (least squares ordinary fit) was also applied when plotted. Overall survival (OS) time were calculated for survival analyses, and the Kaplan–Meier log-rank test was used to compare between-group survival differences. A P-value of less than 0.05 was taken as statistically signifificant for all the analyses.

    Variables with
    P < 0.05 by univariate analysis were selected as covariates for adjustment in multivariate Cox proportional hazards regression model to
    estimate HRs with 95% confidence intervals (95% CI). Events in EFS
    referred to nonresponse to chemotherapy, disease progression,
    relapse, and death. All tests were two-sided; significance levels were
    set to P < 0.05 (), P < 0.01 (), P < 0.001 (), and P < 0.0001 (),
    and NS means not significant. All statistical data were analyzed using
    GraphPad Prism version 7.0 and IBM SPSS Statistics 22.0.

    cellular defense response
    T cell activation involved in immune response
    NK T cell activation
    positive regulation of immune response to tumor cell
    natural killer cell activation

    1. <br />GO:0002708<br />positive regulation of lymphocyte mediated immunity

    GO:0001906
    cell killing

    GO:0002456
    T cell mediated immunity

    GO:0001916
    positive regulation of T cell mediated cytotoxicity

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