Bioinformatics analysis and NFKBIZ expression profile mining in The Cancer Genome Atlas (TCGA)

Relevant data or figures from TCGA database (http://cancergenome.nih.gov) were downloaded and analyzed using the Gene Expression Profiling Interacting Analysis (GEPIA; http://gepia.cancer-pku.cn), UCSC Xena (http://xena.ucsc.edu) and UALCAN (http://ualcan.path.uab.edu) databases. The data from GEPIA included NFKBIZ expression from 404 tumor and 28 adjacent normal control tissues. The data from UCSC Xena included NFKBIZ expression from 407 tumor and 29 adjacent normal control tissues. The data from UALCAN included NFKBIZ expression from 408 tumor and 19 adjacent normal control tissues. NFKBIZ mRNA expression was also explored at different stages, nodal metastasis status and histological subtypes using the UALCAN database. Finally, the 'TCGAbiolinks' package in R language (https://www.rdocumentation.org/packages/TCGAbiolinks/versions/1.2.5) was used to download the mRNA-reads count expression data from TCGA-BLCA, including 408 BC and 19 normal bladder tissue samples. An mRNA expression matrix was made with the raw counts of each RNA in each sample. The 'Deseq2' package in R (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html) was used to calculate the differential expression of mRNAs between the BC tissues samples and paracancerous normal specimens. A |fold-change| >2 and P<0.05 were used as the threshold values. Survival analysis was performed using these differentially expressed mRNAs using the 'ggsurv' package in R (https://www.rdocumentation.org/packages/GGally/versions/1.5.0/topics/ggsurv), with P<0.05 used as the screening threshold. The survival curves based on NFKBIZ expression were used to explore the effect of NFKBIZ expression on survival and prognosis of patients with BC. Kaplan-Meier analysis was used for survival analysis, and the log-rank test was used to calculate the P-values.