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BMC Med. 2012; 10: 39.
Published online Apr 19, 2012. doi:  10.1186/1741-7015-10-39
PMCID: PMC3378448
Bioinformatic identification of proteins with tissue-specific expression for biomarker discovery
Ioannis Prassas,#1,2 Caitlin C Chrystoja,#1 Shalini Makawita,#1,2 and Eleftherios P Diamandiscorresponding author1,2,3
1Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
2Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
3Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
corresponding authorCorresponding author.
#Contributed equally.
Ioannis Prassas: yprassas/at/gmail.com; Caitlin C Chrystoja: cchrystoja/at/gmail.com; Shalini Makawita: shalini.makawita/at/gmail.com; Eleftherios P Diamandis: ediamandis/at/mtsinai.on.ca
Received December 16, 2011; Accepted April 19, 2012.
Abstract
Background
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.
Methods
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.
Results
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.
Conclusions
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.
Keywords: bioinformatics, biomarkers, tissue-specific proteins
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