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[NEW DELHI] By hosting a database that integrates cancer genes and markers with experimental data, researchers at Sri Venkateswara University (SVU) in Tirupati, Andhra Pradesh, have developed a platform to identify genes that are highly expressed in tumours and provide insight into genetic alterations in cancer.
In a paper published last month (July) in Nature Scientific Reports, the research team from SVU’s department of animal biotechnology, describes the need for a database for different genes and markers along with their molecular characteristics and pathway associations.
The Cancer Gene Markers Database (CGMD) provides a platform to better understand tumour genes and markers at a molecular level by integrating them with literature on treatment regimen and recent advances in cancer therapy.
Free to access, the CGMD already includes 309 genes and 206 markers that correspond to 40 different human cancers. Accompanying literature is sourced from well-established databases such as the National Center for Biotechnology Information, Kyoto Encyclopedia of Genes and Genomes and has experimental data from PubMed.
Research has shown that expression of tumour suppressor genes changes with respect to cancer stage and type. Therefore, in addition to tumour genes, data on tumour markers contribute to a clearer picture of cancer stages and types and hence provide valuable clues for identifying genes that are highly expressed in tumours but not in normal tissues.
“To understand biological processes, we must integrate new observations with existing knowledge to create testable models that can be iteratively refined,” says J.A. Pradeepkiran, bioinformatics research scholar at SVU’s animal biotechnology department and an author of the study.
According to Pradeepkiran, the success of the CGMD will depend on the amount of data gathered by large-scale profiling of biological features that can be efficiently integrated with data from literature and databases for better visualisation and analysis.
“Cancer is recognised as a complex system with many genetic and molecular components that are tightly connected through mechanisms that cancer biologists are desperately trying to decipher in order to identify more effective approaches to correct errors and cure the disease,” explains Pradeepkiran.
“An integrated approach to data hosting is an excellent idea,” says Kamal Kumar Gupta, associate professor at the zoology department of Delhi University. “What happens in research is that many times you don’t have integrated data, so time is spent sourcing data from varied sources just to find the right literature.”
Ongoing collection and curation of information on tumour genes and markers and updating the database with new experimental evidence will help better prognosis, prevention and treatment for cancer, the researchers say.
“We believe that this work would significantly contribute to society by better understanding the molecular prospects in developing novel diagnostics kits in cancer biology,” M. Bhaskar, research supervisor at SVU and one of the authors of the paper, tells SciDev.Net.
>Link to paper published in Nature
This article has been produced by SciDev.Net's South Asia desk.
References
Jangampalli Adi, P. et al. CGMD: An integrated database of cancer genes and markers. Sci. Rep. 5, 12035; doi: 10.1038/srep12035 (2015).
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