Finally, the GTPase ERAL1, mitochondrial ribosomal proteins ERAL1, MRPL11, MRPL15, MRPL30, MRPL37, MRPL40, and MRPL52 were determined to be hub proteins with a commonly down-regulated trend in four berberine-treated colon cancer cell lines. Here, MRPL52 is linked to malignant colon neoplasm.