Prognostic Role of TMED3 in Clear Cell Renal Cell Carcinoma: A Retrospective Multi-Cohort Analysis
In this study, we present the first data on TMED3 expression in ccRCC in a well-defined cohort from the TGCA (Cerami et al., 2012; Cancer Genome Atlas Research Network et al., 2013) and ICGC (International Cancer Genome Consortium et al., 2010) primary ccRCC cohorts. The statistical analysis suggested that TMED3 could be a useful prognostic factor in ccRCC.
Materials and Methods
Patient Data Acquisition and Statistical Analysis
The data were downloaded from TCGA (Cerami et al., 2012; Cancer Genome Atlas Research Network et al., 2013) and ICGC (International Cancer Genome Consortium et al., 2010) from the ICGC data portal1 in March 2018. We downloaded mRNA expression (TCGA, RSEM normalization; ICGC, RPKM normalization) and clinical information. Samples with insufficient information (gene expression values and survival information) were excluded from the analysis. GSE11024 (Affymetrix U133 Plus 2.0 Array) (Kort et al., 2008), GSE12606 (Affymetrix U133 Plus 2.0 Array) (Stickel et al., 2009), and GSE14762 (Affymetrix U133 Plus 2.0 Array) (Wang et al., 2009) were downloaded from GEO database using “GEOquery” R package. In the stage-related analysis, only the “Not Available (NA)” value of the stage was excluded. When the grade-related analysis was performed, only the “NA” value of the grade was excluded. These analyses were performed using R software version 3.5.0 (R Core Team, 2018).
To identify the differences of TMED3 expression valu...
Source: Frontiers in Genetics - Category: Genetics & Stem Cells Source Type: research
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