Computational protocol: Pyrimidine metabolic rate limiting enzymes in poorly-differentiated hepatocellular carcinoma are signature genes of cancer stemness and associated with poor prognosis

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Protocol publication

[…] The expression status of metabolic enzymes in liver cancer (LIHC) patients of TCGA was obtained from The Cancer Genome Atlas project (TCGA, https://tcga-data.nci.nih.gov/tcga/). The transcriptome datasets of HCC performed in microarray were downloaded from GEO database. Gene expression was quantified using RSEM (RNA-Seq by Expectation-Maximization) [] and probe intensity for RNA-seq and microarray datasets, respectively. Quantified RNA expression in TCGA is using RSEM a generative model to estimate RNA expression by EM algorithm and available for download. RLE score was calculated based on the sum of expression value of 22 upregulated RLEs or the sum of expression value of 77 downregulated RLEs in TCGA. The two populations of HCC patients with high and low RLE scores were further classified and performed the gene set enrichment analysis (GSEA) and survival analysis by Cutoff finder []. [...] Data was expressed as the mean ± SD. All statistical analyses were conducted using Student's t-test by the SPSS statistical software program (v17.0; SPSS Inc.). Statistical significance was set at *P≤0.05, **P≤0.001 ***p<0.0001 by two-tailed Student's t-test. The chi square test was applied to evaluate the correlation between RLE score and CD44 expression. The high and low populations in RLE score and CD44 expression was selected by first and fourth quantiles respectively. The survival analysis was assessed with cutoff finder at the website http://molpath.charite.de/cutoff/index.jsp []. […]

Pipeline specifications

Software tools RSEM, GSEA, Cutoff Finder, SPSS
Databases TCGA Data Portal
Applications Miscellaneous, RNA-seq analysis
Organisms Homo sapiens
Diseases Carcinoma, Hepatocellular, Liver Neoplasms, Neoplasms, Brain Stem Neoplasms