Colonic cancer has become a main reason of mortality associated with cancer; however, left and right‑sided colonic cancer have diverse outcomes in terms of epidemiological, histological, clinical parameters and prognosis. We aimed to examine the discrepancies between these two types of colon cancers to identify potential therapeutic targets. In the present study, three gene expression profiles (GSE44076, GSE31595, GSE26906) from Gene Expression Omnibus (GEO) database were downloaded and further analyzed. A PPI (protein‑protein interaction) network of the differentially‑expressed genes (DEGs) of GSE44076 between tumor and normal was established with the Search Tool for the Retrieval of Interacting Genes database. Then, the DEGs of these two colon cancers (left, right) samples were identified. Subsequently, the intersection of DEGs of left and right‑sided colon cancer samples obtained from three databases, and DEGs of tumor and normal samples were analyzed. Collagen type XI α1 chain (COL11A1), Twist family bHLH transcription factor 1 (TWIST1), insulin‑like 5 and chromogranin A were upregulated proteins, while 3β‑hydroxysteroid dehydrogenase was downregulated protein in right colon cancer than in left‑sided tumor samples. Through further experimental verification, we revealed that COL11A1 and TWIST1 were significantly upregulated at the mRNA and protein levels within right‑sided colon cancer compared with in left‑sided colon cancer samples (P<0.05), consistent with bioinformatical analysis. Furthermore, a positive correlation between COL11A1 and TWIST1 protein expression was observed (P<0.0276). Collectively, our data showed that COL11A1 and TWIST1 may be potential prognostic indicators and molecular targets for the treatment of right‑sided colon cancer.