Network analysis identifies DAPK3 as a potential biomarker for lymphatic invasion and colon adenocarcinoma prognosis

Abstract

WCGNA reveals a gene module linked to lymphatic invasion in colon adenocarcinoma DAPK3 is a pseudohub gene with differential expression in colon cancerGene ontology identified relationships to cytoskeletal organization and apoptosis DAPK3 was correlated with lymphatic invasion and poor overall survival

Network analysis of TCGA and GTEx gene expression datasets for identification of trait-associated biomarkers in human cancer

“…A volcano plot is a type of scatter plot that illustrates the statistical significance (−log 10 (adjusted p value)) and magnitude of change (log 2 (fold-change)) associated with the conditions under comparison. The volcano plot seen in Figure 5B of Chen and MacDonald (2021) is the expected outcome of differential gene expression analysis on TCGA tumor vs. GTEx normal tissue. The Methods S8 file “ R Markdown Code Script for Enhanced Volcano” contains the exact script used to construct a volcano plot with the refined list (i.e., have undergone treat ) of DEGs saved during step 24 of step-by-step method details using the EnhancedVolcano R package ( Blighe and Lasky-Su, 2021 ).…”

“…Here, we provide protocols to perform differential-expressed gene analysis of TCGA and GTEx RNA-Seq data from human cancers, complete integrative GO and network analyses with focus on clinical and survival data, and identify differential correlation of trait-associated biomarkers. For complete details on the use and execution of this protocol, please refer to Chen and MacDonald (2021) .…”

“…For complete details on the use and execution of this protocol, please refer to Chen and MacDonald (2021) .…”

Targeting Death-Associated Protein Kinases for Treatment of Human Diseases: Recent Advances and Future Directions

“…Therefore, a novel approach for the treatment of Pca may involve the use of both Akt inhibitors and DAPK3 activators, and the combination of the two may result in synergistic results . According to a recent network analysis, DAPK3 has been identified as a potential biomarker for lymphatic invasion and the prognosis of colon cancer, although DAPK3 expression is reduced in patients with colon cancer, but high DAPK3 expression is associated with more significant lymphatic infiltration and poorer survival . Notably, DAPK3 expression levels increased in mesenteric arteries of spontaneously hypertensive rats (SHR).…”

“…22 According to a recent network analysis, DAPK3 has been identified as a potential biomarker for lymphatic invasion and the prognosis of colon cancer, although DAPK3 expression is reduced in patients with colon cancer, but high DAPK3 expression is associated with more significant lymphatic infiltration and poorer survival. 155 Notably, DAPK3 expression levels increased in mesenteric arteries of spontaneously hypertensive rats (SHR). Thus, the inhibition of DAPK3 may serve as a strategy for the treatment of cardiovascular diseases.…”