6 883 Plasmodium PlasmoDB http / / PlasmoDB. org Molecular Functional Annotation Secondary Database PlasmoFADB PlasmoDB PlasmoFADB

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1 Chinese Journal of Biomedical Engineering Vol. 31 No. 6 December 2012 * * J2EE MySQL MVC Web Services Hibernate Fisher's R Gene Ontology Pathway Graphviz Gene Ontology Pathway R318 A The Construction of Pathogenic Plasmodium Molecular Functional Annotation Secondary Database XU San-Gang ZHUANG Yong-Long HAO Zhi-Yong SHAN Guang-Liang YANG Xiao-Lin * WANG Heng * Institute of Basic Medical Sciences Chinese Academy of Medical Sciences School of Basic Medicine Peking Union Medical College Beijing China Abstract This research is intended to annotate functions of the molecules from high-throughput 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. Key words plasmodium molecular functional annotation secondary database doi / j. issn DKA32402 * yangxl74@ gmail. com hengwang@ pumc. edu. cn

2 6 883 Plasmodium PlasmoDB http / / PlasmoDB. org Molecular Functional Annotation Secondary Database PlasmoFADB PlasmoDB PlasmoFADB PlasmoDB plasmodium berghei str. 1 ANKA pbe plasmodium chabaudi ProbeID chabaudi pcb 3D7 plasmodium ID 2 falciparum 3D7 pfa plasmodium ID NCBI knowlesi strain H pkn plasmodium vivax SaI-1 pvx plasmodium yoelii 3 Gene str. 17XNL pyo Ontology Pathway PlasmoFADB GenBank KEGG Gene Ontology GO MINT Uniprot Affymetrix 1 Tab. 1 1 Data sources and download websites URL GenBank 4 http / / www. ncbi. nlm. nih. gov / genbank Gene Ontology 5 ftp / / ftp. geneontology. org / godatabase Goterm Term2term KEGG 6 www. genome. jp / kegg / MINT 7 ftp / / mint. bio. uniroma2. it Uniprot 8 http / / www. uniprot. org / downloads Affymetrix 9 http / / www. affymetrix. com / 1. 2 PlasmoFADB MySQL 1 PlasmoFADB GeneInfo Gene2GO GO Gene2Pathway R Pathway Probe Probe2Gene Probe2GO GO GOTerm GO 3 Term2Term GO Pathway Genecoords Interaction 2 PlasmoFADB GeneID ID KEGG GO MINT

3 PlasmoFADB Fig. 1 Overall structure of the PlasmoFADB Fig. 2 2 PlasmoFADB Topological structure of PlasmoFADB Gene2Pathway Gene2GO Interaction JDBC / Hibernate JAVA ProbeID ID Gene Symbol GeneID TAB R XML q q Fisher's p-value 3 1 XML protein-protein TAB XML interaction PPI TAB 2 MySQL SVG Adobe SVG Viewer PlasmoFADB PlasmoFADB Portal XML PlasmoFADB J2EE MVC PlasmoFADB 10 R Gene Ontology Pathway 11 Graphviz Graph Visualization Software PPI 12 HTML JavaScript Ajax Jquery XML

4 PlasmoFADB GO Pathway 7 2 PlasmoFADB Tab. 2 R Gene 3 PlasmoFADB Ontology Pathway 2 PlasmoFADB Data item number of PlasmoFADB data tables pbe pcb pfa pkn pvx pyo GeneInfo GoTerm Gene2Pathway Pathway Interaction Fig. 3 3 PlasmoFADB Interface of PlasmoFADB molecular functional annotation Hits GO Pathway 2. 1 GO GO Gene2GO GO2Gene GO Pathway2Gene GO PathwayDB GO GO Hits Threshold p q GO 4 Pathway Gene2Pathway Pathway2Gene Gene2Pathway Name GO2Gene GO 6 7 Pathway2Gene show level p q

5 Gene2GO Fig. 4 Tree diagram of Gene2GO Fig. 5 5 GO2Gene The result of GO2Gene enrichment analysis Fig. 6 6 Pathway2Gene The result of Pathway2Gene enrichment analysis

6 6 887 Fig. 7 7 Pathway2Gene The result of Pathway2Gene graphical dynamic display NCBI Threshold Direct layout NCBI ID DB Hits Engine Fig. 8 8 The result of protein interaction network diagram 3 PlasmoDB ID NCBI Gene Ontology Pathway PlasmoFADB PPI ID PlasmoFADB Gene2GO Pathway2Gene PlasmoFADB Gene Ontology Gene Pathway PlasmoFADB R GO Pathway PlasmoFADB SVG PPI

7 Adobe SVG Viewer PPI PPI PPI mirnas mirnas Promoter Transfactor 9 Affymetrix Community. CSV format Release 32 EB / OL 1 Snow RW Uerra CA Noor AM et al. The global distribution of clinical episodes of Plasmodium falciparum malaria J. Nature J Aurrecoechea C Brestelli J Brunk BP et al. PlasmoDB a functional genomic database for malaria parasites J. Nucleic Acids Res D539 - D Benson DA Karsch-Mizrachi I Lipman DJ et al. GenBank J. Nucleic Acids Res D32 - D37. 5 Kanehisa M Goto S Sato Y et al. KEGG for integration and interpretation of large-scale molecular datasets J. Nucleic Acids Res D109 - D The Gene Ontology Consortium. Gene ontology tool for the unification of biology J. Nat Genet Licata L Briganti L Peluso D et al. MINT the molecular interaction database 2012 update J. Nucleic Acids Res D857 - D The UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource UniProt J. Nucleic Acids Res D71 - D75. Plasmodium _ Anopheles Annotations. http / / www. affymetrix. com / estore / support / technical / annotationfilesmain. affx / Web Service J J J