DDEC: Dragon database of genes implicated in esophageal cancer

Handle URI:
http://hdl.handle.net/10754/325254
Title:
DDEC: Dragon database of genes implicated in esophageal cancer
Authors:
Essack, Magbubah ( 0000-0003-2709-5356 ) ; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Seshadri, Sundararajan V; Christoffels, Alan; Kaur, Mandeep; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
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. 2009 Essack et al; licensee BioMed Central Ltd.
KAUST Department:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
Essack M, Radovanovic A, Schaefer U, Schmeier S, Seshadri SV, et al. (2009) DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer 9: 219. doi:10.1186/1471-2407-9-219.
Publisher:
Springer Nature
Journal:
BMC Cancer
Issue Date:
6-Jul-2009
DOI:
10.1186/1471-2407-9-219
PubMed ID:
19580656
PubMed Central ID:
PMC2711974
Type:
Article
ISSN:
14712407
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorEssack, Magbubahen
dc.contributor.authorRadovanovic, Aleksandaren
dc.contributor.authorSchaefer, Ulfen
dc.contributor.authorSchmeier, Sebastianen
dc.contributor.authorSeshadri, Sundararajan Ven
dc.contributor.authorChristoffels, Alanen
dc.contributor.authorKaur, Mandeepen
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2014-08-27T09:42:44Z-
dc.date.available2014-08-27T09:42:44Z-
dc.date.issued2009-07-06en
dc.identifier.citationEssack M, Radovanovic A, Schaefer U, Schmeier S, Seshadri SV, et al. (2009) DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer 9: 219. doi:10.1186/1471-2407-9-219.en
dc.identifier.issn14712407en
dc.identifier.pmid19580656en
dc.identifier.doi10.1186/1471-2407-9-219en
dc.identifier.urihttp://hdl.handle.net/10754/325254en
dc.description.abstractBackground: 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. 2009 Essack et al; licensee BioMed Central Ltd.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectchemical agenten
dc.subjectenzymeen
dc.subjectproteinen
dc.subjecttoxinen
dc.subjecttranscription factoren
dc.subjectcomputer programen
dc.subjectdata miningen
dc.subjectesophagus canceren
dc.subjectgene expressionen
dc.subjectgenetic databaseen
dc.subjectinformation processingen
dc.subjectknowledge baseen
dc.subjectpromoter regionen
dc.subjectbiological modelen
dc.subjectcomputer interfaceen
dc.subjectdata baseen
dc.subjectesophagus tumoren
dc.subjectgene expression profilingen
dc.subjectgene expression regulationen
dc.subjectgeneticsen
dc.subjectinformation retrievalen
dc.subjectmetabolismen
dc.subjectmortalityen
dc.subjectovary tumoren
dc.subjectprotein databaseen
dc.subjecttreatment outcomeen
dc.subjectDatabase Management Systemsen
dc.subjectDatabases, Geneticen
dc.subjectDatabases, Proteinen
dc.subjectEsophageal Neoplasmsen
dc.subjectGene Expression Profilingen
dc.subjectGene Expression Regulation, Neoplasticen
dc.subjectInformation Storage and Retrievalen
dc.subjectModels, Geneticen
dc.subjectOvarian Neoplasmsen
dc.subjectSoftwareen
dc.subjectTreatment Outcomeen
dc.subjectUser-Computer Interfaceen
dc.titleDDEC: Dragon database of genes implicated in esophageal canceren
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalBMC Canceren
dc.identifier.pmcidPMC2711974en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionSouth African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorBajic, Vladimir B.en

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