Related Experiment Video
Updated: Jun 21, 2026
Development of Compendium for Esophageal Squamous Cell Carcinoma
Published on: April 12, 2024
DDEC: Dragon database of genes implicated in esophageal cancer
Magbubah Essack1, Aleksandar Radovanovic, Ulf Schaefer
1South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa. magbubah@sanbi.ac.za
Background:
Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data.
Description:
Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports.
Conclusion:
We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic and non-profit users at http://apps.sanbi.ac.za/ddec/. DDEC will be updated twice a year.
Insights
A new database, DDEC, offers a centralized resource for esophageal cancer (EC) gene information. This tool aids researchers by integrating scattered data and generating novel association hypotheses for improved diagnostics and therapies.
Area of Science:
- Oncology
- Bioinformatics
- Genetics
Background:
- Esophageal cancer (EC) is a leading cause of cancer death due to late detection and limited treatment options.
- Incomplete understanding of EC molecular processes hinders diagnostic and therapeutic advancements.
- Existing research data on EC is fragmented, posing challenges for data mining and accessibility.
Purpose of the Study:
- To develop a comprehensive, integrated knowledge database for esophageal cancer-related information.
- To provide a centralized gateway for accessing and analyzing EC-implicated genes and their associations.
- To complement existing bioinformatics resources and facilitate research in EC genetics.
Main Methods:
- Manual curation of 529 differentially expressed genes in esophageal cancer.
- Analysis of promoter regions and identification of potential transcription factors for curated genes.
- Integration of text-mined and data-mined reports on gene associations (proteins, metabolites, toxins, diseases, etc.).
Main Results:
- Development of the Dragon Database of Genes Implicated in Esophageal Cancer (DDEC).
- DDEC contains 529 curated EC-related genes with detailed information on their regulatory elements and associations.
- The database facilitates the discovery of rare associations and generates novel 'association hypotheses'.
Conclusions:
- DDEC serves as a valuable resource for researchers and clinicians investigating EC genetics.
- The database aims to accelerate the development of improved diagnostics and therapies for esophageal cancer.
- DDEC is freely accessible for academic and non-profit use and will be updated biannually.
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