- Open Access
The Triple-Negative Breast Cancer Database: an omics platform for reference, integration and analysis of triple-negative breast cancer data
Breast Cancer Research volume 16, Article number: 490 (2014)
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’ (Figure 1).
Considering the heterogeneity of breast cancers, we believe the TNBCDb will serve as a platform for selection of therapeutically relevant molecular entities from the tissue and cell line information and also for the selection of appropriate cell lines for evaluation of therapeutic targets in the direction of personalized therapy. We request suggestions from the scientific community to improve and keep this resource up to date with more information/clinical parameters through an online portal . We believe that this initiative will help us to maintain TNBCDb as a global reference, integration and analysis platform for TNBC.
Human epidermal growth factor receptor 2
Triple-negative breast cancer
Triple Negative Breast Cancer Database
Lehmann BD, Bauer JA, Chen X, Sanders ME, Chakravarthy AB, Shyr Y, Pietenpol JA: Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest. 2011, 121: 2750-2767. 10.1172/JCI45014.
Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A: NetSlim: high-confidence curated signaling maps. Database. 2011, 2011: bar032-
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999, 27: 29-34. 10.1093/nar/27.1.29.
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S: AmiGO: online access to ontology and annotation data. Bioinformatics. 2009, 25: 288-289. 10.1093/bioinformatics/btn615.
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A: Human Protein Reference Database – 2009 update. Nucleic Acids Res. 2009, 37: D767-D772. 10.1093/nar/gkn892.
Giles CB, Girija-Devi R, Dozmorov MG, Wren JD: mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis. BMC Bioinformatics. 2013, 14: S17-10.1186/1471-2105-14-S14-S17.
Triple-Negative Breast Cancer Database FAQ. , [www.tnbcdb-rgcb-res.in/faq.php]
The authors acknowledge the support and suggestions from Professor Beela Sarah Mathew of the Regional Cancer Centre, Thiruvananthapuram, India and from Dr TR Santosh Kumar and Dr KB Harikumar of the Rajiv Gandhi Centre for Biotechnology, Poojappura, Thiruvananthapuram, India. GR is supported by the Indian Council of Medical Research’s Viral Disease Network Program (VIR/8/2011-ECD-1 to RGD), and AMP, AV and BG are supported by grants from Department of Biotechnology, India (BT/PR14209/BID/07/328/2010 and BT/PR5890/BID/7/407/2012). The authors thank all contributors of data.
The authors declare that they have no competing interests.
RG, MRP and RR conceived and designed the study. RR, AMP and VA screened the articles and documented the information. AMP, VA, BG, LR and MV were involved in the development of the website. All authors read and approved the final manuscript.
Authors’ original submitted files for images
Below are the links to the authors’ original submitted files for images.
About this article
Cite this article
Raju, R., Paul, A.M., Asokachandran, V. et al. The Triple-Negative Breast Cancer Database: an omics platform for reference, integration and analysis of triple-negative breast cancer data. Breast Cancer Res 16, 490 (2014). https://doi.org/10.1186/s13058-014-0490-y
- Breast Cancer
- Estrogen Receptor
- Human Epidermal Growth Factor Receptor
- Molecular Entity
- TNBC Cell