In-silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases

Blood protein markers have been studied for the clinical management of cancer. Due to the large number of the proteins existing in blood, it is often necessary to pre-select potential protein markers before experimental studies. However, to date there is a lack of automated method for in-silico selection of cancer blood proteins that integrates the information from both genetic and proteomic studies in a cancer-specific manner. In this work, we synthesized both genomic and proteomic information from several open access databases and established a bioinformatic pipeline for in-silico selection of blood plasma proteins overexpressed in specific type of cancer. We demonstrated the workflow of this pipeline with an example of breast cancer, while the methodology was applicable for other cancer types. With this pipeline we obtained 10 candidate biomarkers for breast cancer. The proposed pipeline provides a useful and convenient tool for in-silico selection of candidate blood protein biomarkers for a variety of cancer research.