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  • br Materials and methods br

    2022-08-31


    2. Materials and methods
    2.1. The mRNA U 46619 of CXCR members in the cancer genome atlas (TCGA)
    The mRNA expression of CXCR family members in TCGA was ana-lyzed via the Gene Expression Profiling Interactive Analysis (GEPIA) platform (http://gepia.cancer-pku.cn/index.html) [22]. The genomic alterations of CXCR members in TCGA, including missense mutation, truncating mutation, amplification and deep deletion, were identified by the cBioPortal platform (http://www.cbioportal.org/) [23,24]. Moreover, the mRNA expression profile of CXCR members was re-trieved from the Xena system for statistical analysis [25].  Cytokine 123 (2019) 154785
    Table 2
    Genetic alterations of CXCR family members in the stomach adenocarcinoma (STAD) of TCGA.
    Cases
    CXCR1 Amplification 3
    Deep deletion 1
    Missense mutation 8
    Amplification 2
    Deep deletion 1
    Missense mutation 6
    Amplification 1
    CXCR4 Amplification 1
    CXCR5 Deep deletion 1
    Amplification 4
    Deep deletion 1
    Missense mutation 4
    Truncating mutation 1
    Amplification 1
    Deep deletion 3
    Missense mutation 2
    Deep deletion 3
    Missense mutation 6
    2.2. Protein-protein interaction (PPI) networks of CXCR members
    The PPI networks of CXCR members were established by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, http:// www.string-db.org/) [26].
    2.3. Oncomine analysis
    The mRNA expression of CXCR members in GC was also explored via the oncomine platform (www.oncomine.org) [27]. The statistical significant cutoff p value was 0.05. The significantly differentially ex-pressed CXCR members between normal and tumor in GC were iden-tified in seven datasets via oncomine [28–33].
    2.4. Survival analysis of CXCR members
    The prognostic values of OS in CXCR members were investigated via the Kaplan-Meier plotter (KM plotter) (www.kmplot.com) [34].
    Fig. 2. The prognostic values of CXCR members in all GC by the KM plotter. (A–G) The prognostic values of CXCR members.
    Furthermore, given the increasing focus on the prognostic values of genes signature, the prognostic value of CXCR signature was also ex-plored via the SurvExpress platform (http://bioinformatica.mty.itesm. mx:8080/Biomatec/SurvivaX.jsp) [35]. High and low risk groups were divided based on the maximized risk algorithm [35].
    2.5. Immune infiltrates correlation via the Tumor Immune Estimation Resource (TIMER)
    The correlations between each immune infiltrates (B cells, CD4+T cells, CD8+T cells, neutrophils, macrophages and dendritic cell types) and CXCR members were analyzed via the TIMER web-based platform (https://cistrome.shinyapps.io/timer/) [36]. The correlation was ex-hibited by the purity-corrected partial Spearman method (partial-cor).
    2.6. DNA methylation data of CXCR members
    The DNA methylation sites of CXCR members in TCGA were ana-lyzed by MethSurv (https://biit.cs.ut.ee/methsurv/), a comprehensive bioinformatics platform for methylation visualization [37]. Meanwhile, the prognostic values of all the methylation sites associated with CXCR members were also characterized.
    2.7. Statistical analysis
    Univariate and multivariate cox analysis of CXCR members was performed in both OS and recurrence-free survival (RFS) with hazard ratio (HR) and 95% confidence interval (95%CI). Nomogram models of OS and RFS were established based on the multivariate results using the R software (version 3.3.0) (R foundation for statistical computing, Vienna, Austria, www.r-project.org). P < 0.05 was considered as sig-nificant. The concordance index (C-index) was used to measure the