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Bioinformatic identification of proteins with tissue-specific expression for biomarker discovery

Ioannis Prassas12, Caitlin C Chrystoja1, Shalini Makawita12 and Eleftherios P Diamandis123*

Author affiliations

1 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada

2 Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada

3 Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada

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Citation and License

BMC Medicine 2012, 10:39  doi:10.1186/1741-7015-10-39

Published: 19 April 2012



There is an important need for the identification of novel serological biomarkers for the early detection of cancer. Current biomarkers suffer from a lack of tissue specificity, rendering them vulnerable to non-disease-specific increases. The present study details a strategy to rapidly identify tissue-specific proteins using bioinformatics.


Previous studies have focused on either gene or protein expression databases for the identification of candidates. We developed a strategy that mines six publicly available gene and protein databases for tissue-specific proteins, selects proteins likely to enter the circulation, and integrates proteomic datasets enriched for the cancer secretome to prioritize candidates for further verification and validation studies.


Using colon, lung, pancreatic and prostate cancer as case examples, we identified 48 candidate tissue-specific biomarkers, of which 14 have been previously studied as biomarkers of cancer or benign disease. Twenty-six candidate biomarkers for these four cancer types are proposed.


We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. Investigation of the 26 candidates in disease states of the organs is warranted.

bioinformatics; biomarkers; tissue-specific proteins