Raju, Rajesh and Mary Paul, Aswathy and Asokachandran, Vivekanand and George, Bijesh and Radhamony, Lekshmi and Vinaykumar, Meena (2014) The Triple-Negative Breast Cancer Database: an omics platform for reference, integration and analysis of triple-negative breast cancer data. Breast Cancer Research, 16 (6). ISSN 1465-542X

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Abstract

Clustering the transcriptomic profile of 587 triple-negative breast cancer (TNBC) cases extracted from 21 breast cancer microarray datasets relying on the lack of transcript-level expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (Her2), Lehmann and colleagues have categorized the TNBCs into seven subgroups . From more than 1,000 clinical samples that were characterized as TNBCs by immunohistochemistry, we report the first compendium of molecular expression-level alterations as a value-added resource for extended research. This open-access manually curated resource, the Triple Negative Breast Cancer Database (TNBCDb) , currently hosts 144 microRNA, 2,696 mRNA, 106 protein and 13 post-translational modification alterations in TNBC tissues. The TNBC tissues are categorized into lymph node-positive, lymph node-negative and lymph node metastatic tissues, or otherwise as TNBC-not specified. TNBCDb hosts experimentally reported alterations in these tissues compared with ER+, ER+PR+, Her2+, ER+PR+Her2−, ER−PR−Her2+, luminal A, luminal B and non-TNBC (if not specified) or matched adjacent normal, unmatched normal breast or parenchyma tissues as analyzed. The ethnicity/origin as provided by the authors/deduced, the frequency of observation of the molecular alterations in terms of the number of patient samples analyzed per study, fold values of expression, experiment platform used and the reference to corresponding research articles are provided for the curated records. TNBCDb also hosts the comparative molecular profile of 39 TNBC cell lines compared among themselves as well as with 55 non-TNBC cell lines as a tool for selection of appropriate cell lines for specific studies on the basis of their molecular background. Effective visualization of genes differentially regulated in TNBC tissues and cell lines and, further, the signaling pathways , biological processes, molecular functions, cellular localization , protein–protein interactions , microRNA targets and RNA-level co-expressed genes that are associated with each type of molecule, is enhanced through unique features designated the ‘TNBCDb viewer’ and the ‘Network viewer’ .

Item Type:	Article
Uncontrolled Keywords:	Triple-negative breast cancer, Triple Negative Breast Cancer Database, TNBC, Estrogen receptor, Progesterone receptor, Human epidermal growth factor receptor 2
Subjects:	Computational Biology
Depositing User:	DR RESHMI GIRIJADEVI
Date Deposited:	16 Dec 2015 05:30
Last Modified:	22 Dec 2016 05:43
URI:	http://rgcb.sciencecentral.in/id/eprint/31

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