Functional Enrichment Analysis and Cell Immune Infiltration

A comprehensive knowledge-base update to the sixth version of the original web-based programs is provided by the Database for Annotation, Visualization and Integrated Discovery (DAVID, v6.8, https://david.ncifcrf.gov/). With the comprehensive set of function annotation tools provided by DAVID, researchers can examine the biological meanings of a large set of genes. The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products (16). The knowledge of GO resource is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research. DAVID was used to conduct GO analysis based on genes in a univariate Cox analysis of OS and DFS.

Tumor Immune Estimation Resource (TIMER; https://cistrome.shinyapps.io/timer/) is a web interactive platform and is used to analyse tumor-infiltrating immunocytes systematically. We utilized TIMER to study the correlation of genes in the risk score model and the signatures of tumor-infiltrating immunocytes in COAD. The “Gene” module was carried out to investigate the relevance between the risk score model expression and immunocyte infiltration levels specific to each gene (B-cells, neutrophils, macrophages, dendritic cells, CD4+ and CD8+ T-cells) with the TCGA database. We applied TIMER to explore the relationship between the gene expression in the risk score model and the marker gene sets of different immunocytes with the “Correlation” module. The relationship between the gene expression in the risk score model and the tumor-infiltrating immune cells were assessed by purity-correlated partial Spearman's correlation and statistical significance (17).