This article is part of the supplement: Ninth International Conference on Bioinformatics (InCoB2010): Computational Biology

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iCOD : an integrated clinical omics database based on the systems-pathology view of disease

Kazuro Shimokawa1*, Kaoru Mogushi1, Satoshi Shoji1, Atsuko Hiraishi1, Keisuke Ido1, Hiroshi Mizushima1* and Hiroshi Tanaka12

Author Affiliations

1 Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan

2 Department of Bioinformatics and Computational Biology School of Biomedical Science, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan

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BMC Genomics 2010, 11(Suppl 4):S19  doi:10.1186/1471-2164-11-S4-S19

Published: 2 December 2010



Variety of information relating between genome and the pathological findings in disease will yield a wealth of clues to discover new function, the role of genes and pathways, and future medicine. In addition to molecular information such as gene expression and genome copy number, detailed clinical information is essential for such systematic omics analysis.


In order to provide a basic platform to realize a future medicine based on the integration of molecular and clinico-pathological information of disease, we have developed an integrated clinical omics database (iCOD) in which comprehensive disease information of the patients is collected, including not only molecular omics data such as CGH (Comparative Genomic Hybridization) and gene expression profiles but also comprehensive clinical information such as clinical manifestations, medical images (CT, X-ray, ultrasounds, etc), laboratory tests, drug histories, pathological findings and even life-style/environmental information. The iCOD is developed to combine the molecular and clinico-pathological information of the patients to provide the holistic understanding of the disease. Furthermore, we developed several kinds of integrated view maps of disease in the iCOD, which summarize the comprehensive patient data to provide the information for the interrelation between the molecular omics data and clinico-pathological findings as well as estimation for the disease pathways, such as three layer-linked disease map, disease pathway map, and pathome-genome map.


With these utilities, our iCOD aims to contribute to provide the omics basis of the disease as well as to promote the pathway-directed disease view. The iCOD database is available online, containing 140 patient cases of hepatocellular carcinoma, with raw data of each case as supplemental data set to download. The iCOD and supplemental data can be accessed at webcite