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GICDB:An Oncogenomic Database of Gastrointestinal Cancer


Affiliations
1 Sub-Distributed Informatics Centre of Bioinformatics, National Institute of Technology, Raipur 492 010, India
 

Gastrointestinal Cancer Database (GICDB) is a repository of genetic association studies on gastrointestinal cancer which allows researchers to interpret the risk factors of the disease accurately and provide new insights towards further work. GICDB has been developed to provide a platform to clinicians and researchers for the easy retrieval of appropriate information. All data are stored and managed in MySQL and web interface has been developed in ASP. Currently, the database integrates information of 463 genes and 713 miRNA; these genes are implicated in the diverse phases of various gastrointestinal (GI) cancers. GICDB is distinct from other databases in that: (i) it consists of information on genes and miRNAs involved in various GI cancers; (ii) data in GICDB are linked to other on-line resources such as Entrez, Ensemble, UniGene, Swiss-Prot and On-Line Mendelian Inheritance in Man; (iii) there is information on GI cancer-associated drugs retrieved from DrugBank, and (iv) it also integrates the information related to medicinal plants and their use in the treatment of different GI cancers with the structure of their chemical constituents. Unambiguously this database would provide a platform to retrieve genuine information for researchers working on GI cancer. GICDB can be freely accessed at http://gidb.subdic-bioinformatics-nitrr.in/.

Keywords

Gastrointestinal Cancer, Oncogenomic Database, Genes and miRNAs.
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  • Leo, S. et al., Carr systemic treatment of gastrointestinal cancer in elderly patients. J. Gastrointest. Cancer, 2013, 44(1), 22–32.

  • Yamada, T. et al., Textbook of Gastroenterology, Blackwell Chichester, West Sussex, 2009, 5th edn, pp. 603, 1028; ISBN 978-1-4051-6911-0. OCLC 404100761 (https://www.worldcat.org/oclc/404100761).

  • Bjelakovic, G. 1, Nikolova, D., Simonetti, R. G. and Gluud, C., Antioxidant supplements for prevention of gastrointestinal cancers: a systematic review and meta-analysis. Lancet, 2004, 364(9441), 1219–1228.

  • Rebecca, L., Siegel, MPH1* and Kimberly, D., Miller, MPH2; Ahmedin Jemal, DVM, PhD3 Cancer Statistics, CA: Cancer J. Clin., 2015, 65(1), 5–29.

  • Boland, C. R., The molecular biology of gastrointestinal cancer: implications for diagnosis and therapy. Gastrointest. Endosc. Clinics North Am., 2008, 18(3), 401-vii; doi:10.1016/j.giec.2008.03.003.

  • Langho, L. et al., Liverome: a curated database of liver cancerrelated gene signatures with self-contained context information. BMC Genom., 2011, 12, S3; doi:10.1186/1471-2164-12-S3-S3.

  • Chelala, C. et al., Crnogorac-Jurcevic pancreatic expression database: a generic model for the organization, integration and mining of complex cancer datasets. BMC Genom., 2007, 8, 439.

  • Essack, M. I. et al., DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer, 2009, 9, 219; doi:10.1186/1471-2407-9-219.

  • Maglott, D., Ostell, J., Pruitt, K. D. and Tatusova, T., Entrez Gene: gene centered information at NCBI. Nucleic Acids Res., 2007, 35, D26–D31.

  • Safran, M. et al., GeneCards: towards a complete, object-oriented, human gene compendium. Bioinformatics, 2002, 18, 1542–1543.

  • Amberger, J., Bocchini, C. A., Scott, A. F. and Hamosh, A., McKusick’s Online mendelian inheritance in man (OMIM). Nucleic Acids Res., 2009, 37, D793–D796.

  • Pedro, M., Costa 1, 2 and Maria, C. Pedroso de Lima MicroRNAs as Molecular Targets for Cancer Therapy: On the Modulation of MicroRNA Expression. Pharmaceuticals, 2013, 6, 1195–1220.

  • Wishart, D. S. et al., DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 2008 36, D901–D906.

  • Hatfield, C. L., May, S. K. and Markoff, J. S., Quality of consumer drug information provided by four Web sites. Am. J. Health Syst. Pharm., 1999, 56, 2308–2311.

  • Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. and Hirakawa, M., KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 2010, 38, D355–D360.

  • Sayers, E. W. et al., Database resources of the national center for biotechnology information. Nucleic Acids Res., 2010, 38, D5–D16.

  • Hodge, A. E., Altman, R. B. and Klein, T. E., The PharmGKB: integration, aggregation, and annotation of pharmacogenomic data and knowledge. Clin. Pharmacol. Ther., 2007, 81, 21–24.

  • Mouli, K. C., Vijaya, T. and Rao, S. D., Phytoresources as potential therapeutic agents for cancer treatment and prevention. J. Global Pharma Technol., 2009, 1(1), 4–18.

  • Barbosa, L. C., Garrido, S. S. and Marchetto, R., BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems. Comput. Biol. Med., 2015, 58C, 146–153.

  • Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A. and Enright, A. J., miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 2005, 34, D140–D144.

  • Maqungo, M. et al., Bajic DDPC: dragon database of genes associated with prostate. Cancer Nucleic Acids Res., 2010, 1–6.

  • Dhanamani, M., Lakshmi Devi, S. and Kannan, S., Ethnomedicinal plants for cancer therapy – a review. J. Drugs Med., 2011, 3(1), 1–10.


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  • GICDB:An Oncogenomic Database of Gastrointestinal Cancer

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Authors

Jyotsna Choubey
Sub-Distributed Informatics Centre of Bioinformatics, National Institute of Technology, Raipur 492 010, India
Jyoti Kant Choudhari
Sub-Distributed Informatics Centre of Bioinformatics, National Institute of Technology, Raipur 492 010, India
Ashish Patel
Sub-Distributed Informatics Centre of Bioinformatics, National Institute of Technology, Raipur 492 010, India
M. K. Verma
Sub-Distributed Informatics Centre of Bioinformatics, National Institute of Technology, Raipur 492 010, India

Abstract


Gastrointestinal Cancer Database (GICDB) is a repository of genetic association studies on gastrointestinal cancer which allows researchers to interpret the risk factors of the disease accurately and provide new insights towards further work. GICDB has been developed to provide a platform to clinicians and researchers for the easy retrieval of appropriate information. All data are stored and managed in MySQL and web interface has been developed in ASP. Currently, the database integrates information of 463 genes and 713 miRNA; these genes are implicated in the diverse phases of various gastrointestinal (GI) cancers. GICDB is distinct from other databases in that: (i) it consists of information on genes and miRNAs involved in various GI cancers; (ii) data in GICDB are linked to other on-line resources such as Entrez, Ensemble, UniGene, Swiss-Prot and On-Line Mendelian Inheritance in Man; (iii) there is information on GI cancer-associated drugs retrieved from DrugBank, and (iv) it also integrates the information related to medicinal plants and their use in the treatment of different GI cancers with the structure of their chemical constituents. Unambiguously this database would provide a platform to retrieve genuine information for researchers working on GI cancer. GICDB can be freely accessed at http://gidb.subdic-bioinformatics-nitrr.in/.

Keywords


Gastrointestinal Cancer, Oncogenomic Database, Genes and miRNAs.

References





DOI: https://doi.org/10.18520/cs%2Fv112%2Fi09%2F1822-1825