Background: Cancer stem cells (CSCs) are involved in the development of cancer. This study aimed to identify hallmark genes associated with the adjustment of CSC properties.Methods: The COAD data from The Cancer Genome Atlas(TCGA) database were assessed based on the mRNA stemness index (mRNAsi) and corrected mRNAsi. Then, both of them were analyzed with differentially expressed genes (DEGs). The gene modules were pinpointed through weighted gene co-expression network analysis (WGCNA). The genes of the most interest module were functionally annotated through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The Search Tool for the Retrieval of Interacting Genes (STRING) was adopted to obtain protein-protein interaction (PPI) networks, and the hub genes were identified in the light of the Molecular Complex Detection (MCODE) and Cytoscape plugin cytoHubba. Upstream genes were analyzed via the DisNor. In addition, the associations between clinical variables and hub genes were estimated. The bioinformatic results were verified based on Gene Expression Profling Integrative Analysis (GEPIA), Oncomine and Gene Expression Omnibus (GEO). Finally, the protein expression of the hub genes was verified by western blotting.Results: Both the corrected mRNAsi and mRNAsi increased within COAD tissues relative to those within normal colon tissues, which showed a significantly decreasing trend in COAD as the clinical stage. GO indicated the biological processes, including muscle cell differentiation, multicellular organismal signaling, muscle system process and muscle contraction. KEGG revealed Tight junction, Dilated cardiomyopathy (DCM), Vascular smooth muscle contraction, and the cGMP PKG signal transduction pathway. The seven hub genes (ACTA2, CALD1, LMOD1, MYL9, MYLK, TAGLN and TPM2) were identified in the brown module. Most of them were associated with clinical stage; MYL9, TAGLN and TPM2 were associated with overall survival. TGFB1, SRF, ROCK1 and PRKCA were the upstream genes through the DisNor. In the Oncomine, GEO and GEPIA databases, the expression of seven hub genes were down-regulated. In TCGA and GEPIA databases, the tendency of the seven hub genes was decreased with the advance in stage. Conclusions: The hub genes identified in the present study meight play a vital role in the preservation of COAD stem cells.