|
|
|
| The Construction of Pathogenic Plasmodium Molecular Functional Annotation Secondary Database |
| Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China |
|
|
|
Abstract This research is intended to annotate functions of the molecules from highthroughput experimental data produced in the study of pathogenic plasmodium molecular mechanism. J2EE, MySQL, MVC architecture, Web Services and Hibernate techniques were applied to construct a secondary database (PlasmoFADB). Fisher's exact test was utilized for enrichment analysis of Gene Ontology and Pathway. Graphviz tool was used to provide a graphic description for protein-protein interaction. The PlasmoFADB provides a variety of molecular annotation types and displays the annotation results of Gene Ontology, Pathway and PPI with graphic interface. The establishment of the database is a valuable tool to understand the gene functions, signaling pathway in pathogenic plasmodium and helpful for its malaria vaccine antigen screening.
|
|
|
|
|
|
［1］Snow RW, Uerra CA, Noor AM, et al. The global distribution of clinical episodes of Plasmodium falciparum malaria ［J］. Nature, 2005, 434(7030): 214-217.
［2］彭桂英, 王恒. 恶性疟候选疫苗研究进展 ［J］. 国际医学寄生虫病学杂志, 2007, 34(1): 37-42.
［3］Aurrecoechea C, Brestelli J, Brunk BP, et al. PlasmoDB: a functional genomic database for malaria parasites ［J］. Nucleic Acids Res, 2009, 37: D539-D543.
［4］Benson DA, KarschMizrachi I, Lipman DJ, et al. GenBank ［J］. Nucleic Acids Res, 2011, 39: D32-D37.
［5］Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of largescale molecular datasets ［J］. Nucleic Acids Res, 2012, 40: D109-D114.
［6］The Gene Ontology Consortium. Gene ontology: tool for the unification of biology ［J］. Nat Genet, 2000, 25(1): 25-29.
［7］Licata L, Briganti L, Peluso D, et al. MINT, the molecular interaction database: 2012 update ［J］. Nucleic Acids Res, 2012, 40: D857-D861.
［8］The UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt) ［J］. Nucleic Acids Res, 2012, 40: D71-D75.
［9］Affymetrix Community. Plasmodium_Anopheles Annotations, CSV format, Release 32 ［EB/OL］. http://www.affymetrix.com/estore/support/technical/annotationfilesmain.affx, 2011-06-22/2012-11-02.
［10］张智, 张正国. 基于Web Service的生物学实体映射数据库［J］. 中国生物医学工程学报, 2010, 295): 704-709.
［11］曹文君, 李运明, 陈长生. 基因表达谱富集分析方法研究进展 ［J］. 生物技术通讯, 2008, 19(6): 931-934.
［12］张智, 张正国. 基于元数据的异构蛋白质蛋白质相互作用数据库整合［J］. 中国生物医学工程学报, 2010, 29(2): 201-206.
|
|
|
|
