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[NEW DELHI] Researchers in Andhra Pradesh have developed a database to identify genes that are common in tumours to provide their colleagues with easy access to insights into the genetic alterations in cancer.
The database, hosted at the Sri Venkateswara University (SVU) in Tirupati, will integrate information on cancer genes and markers with experimental data.
The Cancer Gene Markers Database (CGMD) is meant to help scientists better understand tumour genes and markers at a molecular level by combining data with literature on treatment regimen and recent advances in cancer therapy.
The database is free to access, and already includes 309 genes and 206 markers that correspond to 40 different human cancers. Accompanying literature comes from databases such as the United States’ National Center for Biotechnology Information and the Kyoto Encyclopedia of Genes and Genomes. It also includes experimental data from PubMed.
In a paper published last month in Nature Scientific Reports, the researchers 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.
“To understand biological processes, we must integrate new observations with existing knowledge to create testable models that can then be refined,” says Pradeepkiran, bioinformatics research scholar at SVU’s animal biotechnology department and an author of the study.
“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, SVU
As research on cancer is progressing it has become clearer that the type of tumour suppressor genes changes with respect to cancer stage and type, the researchers state. Therefore, in addition to tumour genes, data on tumour markers is necessary to get a clearer picture of cancer stages and types. This information provide valuable clues for identifying genes that are highly expressed in tumours but not in normal tissues, they say.
“An integrated approach to data hosting is an excellent idea,” says Kamal Kumar Gupta, an 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.”
The database will continuously collect and curate information on tumour genes and markers and include new experimental evidence. The researchers hope this will improve prognosis, prevention and treatment for cancer.“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.
According to Pradeepkiran, the success of the database will depend on the amount of data that can be gathered by large-scale profiling of biological features, and on whether this information can be integrated with data from literature and databases for better visualisation and analysis.
Jangampalli Adi, P. et al. CGMD: An integrated database of cancer genes and markers. Sci. Rep. 5, 12035; doi: 10.1038/srep12035 (2015).