Chapter 2 : PlasmoDB: The Genome Resource

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The Genome Database was introduced in 2000, in response to emerging needs of the malaria research community for access to genomic-scale datasets. In its earliest manifestations, prior to completion of the genome sequence and curated annotation, PlasmoDB focused on automated analysis of available sequence data, enabling researchers to identify draft sequences for specific genes of interest, even in the absence of the surrounding genomic context. The availability of an effectively complete genome sequence has stimulated a wide range of functional genomics research, and PlasmoDB has endeavored to keep pace with these studies, providing access to the underlying datasets, and allowing a variety of integrative queries, e.g., finding all genes for which both transcript and proteomics data suggest expression in gametocyte stage parasites. PlasmoDB will continue to integrate new datasets as they emerge, developing tools of interest to the malaria researcher and facilitating the discovery of new diagnostics, drugs, and vaccines. PlasmoDB provides the user with a variety of analysis tools for examining and extracting information from the genome and predicted proteome, using BLAST, electronic PCRs, defined motif searches, and tools for the analysis of microarray and proteomics data. Gene Pages provide an encyclopedic view of the genome, where it is possible to look up all information about a specified gene. parasites may be gleaned by browsing the genome in Sequence View mode, and information on specific genes may be obtained from the various Gene Pages.

Citation: Whetzel P, Date S, Gajria K, Fraunholz M, Gajria B, Grant G, Iodice J, Labo P, Milgram A, Stoeckert C, Roos D, Kissinger J. 2005. PlasmoDB: The Genome Resource, p 12-23. In Sherman I (ed), Molecular Approaches to Malaria. ASM Press, Washington, DC. doi: 10.1128/9781555817558.ch2
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Gene Queries using PlasmoDB. A wide variety of dynamic queries may be formulated to interrogate the PlasmoDB database, using pull-down menus available on the home page (also accessible via the Queries button on the blue tool bar, via the help and tutorial pages, and from links at relevant locations throughout the site). Three queries are shown, focused on characteristics that might be of interest to researchers seeking to mine the database for candidate vaccine antigens: (i) a search for genes predicted to encode a secretory signal sequence, (ii) a search for genes that are abundantly transcribed in late schizonts, and (iii) a search for genes that are conserved in but not in the human or mouse genomes.

Citation: Whetzel P, Date S, Gajria K, Fraunholz M, Gajria B, Grant G, Iodice J, Labo P, Milgram A, Stoeckert C, Roos D, Kissinger J. 2005. PlasmoDB: The Genome Resource, p 12-23. In Sherman I (ed), Molecular Approaches to Malaria. ASM Press, Washington, DC. doi: 10.1128/9781555817558.ch2
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Image of FIGURE 2

Integrating gene queries by using the History function. The History page, accessible via the blue tool bar at the top of each page, provides a list of all queries conducted during the current session. Using the boxes at left to specify individual queries of continuing interest permits these datasets to be combined (union), subtracted, or intersected. Intersecting the three queries defined in Figure 1 yields 20 genes that satisfy the specified criteria with respect to phylogenetic distribution, expression, and predicted subcellular location. This list includes merozoite surface protein 1, apical membrane antigen 1, and numerous hypothetical proteins that may warrant further investigation as candidate vaccine antigens.

Citation: Whetzel P, Date S, Gajria K, Fraunholz M, Gajria B, Grant G, Iodice J, Labo P, Milgram A, Stoeckert C, Roos D, Kissinger J. 2005. PlasmoDB: The Genome Resource, p 12-23. In Sherman I (ed), Molecular Approaches to Malaria. ASM Press, Washington, DC. doi: 10.1128/9781555817558.ch2
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1. Altschul, S. F.,, T. J. Madden,, A. A. Schaffer,, J. Zhang,, Z. Zhang,, W. Miller,, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389 3402.
2. Bahl, A.,, B. P. Brunk,, R. L. Coppel,, J. Crabtree,, S. J. Diskin,, M. J. Fraunholz,, G. Grant,, D. Gupta,, R. L. Huestis,, J. C. Kissinger,, P. Labo,, L. Li,, S. K. McWeeney,, A. J. Milgram,, D. S. Roos,, J. Schug,, and C. J. Stoeckert, Jr. 2002. PlasmoDB: the Plasmodium genome resource.An integrated database providing tools for accessing and analyzing mapping, expression and sequence data (both finished and unfinished). Nucleic Acids Res. 30: 87 90.
3. Bahl, A.,, B. P. Brunk,, J. Crabtree,, M. J. Fraunholz,, B. Gajria,, H. Ginsburg,, G. R. Grant,, D. Gupta,, J. C. Kissinger,, P. Labo,, L. Li,, M. D. Mailman,, A. J. Milgram,, D. S. Pearson,, D. S. Roos,, J. Schug,, C. J. Stoeckert, Jr.,, and P. Whetzel. 2003. PlasmoDB: the Plasmodium genome resource. Tools for integrating experimental and computational data. Nucleic Acids Res. 31: 212 215.
4. Bender, A,, G. G. van Dooren,, S. A. Ralph,, G. I. McFadden,, and G. Schneider. 2003. Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum. Mol. Biochem. Parasitol . 132: 59- 66.
5. Berry, A. E.,, M. F. Gardner,, G. J. Caspers,, D. S. Roos,, and M. Berriman. 2004. Curation of the Plasmodium falciparum genome. Trends Parasitol . 20: 548 552.
6. Bozdech, Z.,, M. Llinas,, B. L. Pulliam,, E. D. Wong,, J. Zhu,, and J. L. DeRisi. 2003. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 1: 85 100.
7. Carlton, J. 2003. Plasmodium vivax genome sequencing project. Trends Parasitol . 19: 227 231.
8. Carlton, J.,, J. Silva,, and N. Hall. 2005. The genome of model malaria parasites, and comparative genomics. Curr. Issues Mol. Biol. 7: 23 37.
9. Coppel, R. L.,, D. S. Roos,, and Z. Bozdech. 2004. The genomics of malaria infection. Trends Parasitol . 20: 553 557.
10. Date, S.V.,, and E. M. Marcotte. 2003. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol . 21: 1055 1062.
11. Davidson, S.,, J. Crabtree,, B. P. Brunk,, J. Schug,, V. Tannen,, G. C. Overton,, and C. J. Stoeckert. 2001. K2/Klesli and GUS: experiments in integrated access to genomic data sources. IBM Syst. J. 40: 512 531.
12. Doolan, D. L.,, S. Southwood,, D. A. Freilich,, J. Sidney,, N. L. Graber,, L. Shatney,, L. Bebris,, L. Florens,, C. Dobano,, A.A. Witney,, E. Appella,, S. L. Hoffman,, J. R. Yates III,, D. J. Carucci,, and A. Sette. 2003. Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc. Natl. Acad. Sci. USA 100: 9952 9957.
13. Florens, L.,, M. P. Washburn,, J.D. Raine,, R.M. Anthony,, M. Grainger,, J. D. Haynes,, J. K. Moch,, N. Muster,, J. B. Sacci,, D. L. Tabb,, A.A. Witney,, D. Wolters,, Y. Wu,, M. J. Gardner,, A.A. Holder,, R. E. Sinden,, J. R. Yates,, and D. J. Carucci. 2002. A proteomic view of the Plasmodium falciparum life cycle. Nature 419: 520 526.
14. Florens, L.,, X. Liu,, Y. Wang,, S. Yang,, O. Schwartz,, M. Peglar,, D. J. Carucci,, J. R. Yates,, and Y. Wu. 2004. Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes. Mol. Biochem. Parasitol . 135: 1 11.
15. Foth, B. J.,, S. A. Ralph,, C. J. Tonkin,, N. Struck,, M. J. Fraunholz,, D. S. Roos,, A. F. Cowman,, and G. I. McFadden. 2003. Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum. Science 299: 705 708.
16. Gardner, M. J.,, N. Hall,, E. Fung,, O. White,, M. Berriman,, R. Hyman,, J. Carlton,, A. Pain,, K. E. Nelson,, S. Bowman,, I. T. Paulsen,, K. James,, J. A. Eisen,, K. Rutherford,, S. Salzberg,, A. Craig,, V. Nene,, S. Shallom,, B. Suh,, J. Peterson,, S. Angiuoli,, M. Pertea,, J. Allen,, J. Selengut,, D. Haft,, A. Vaidya,, A. Fairlamb,, D. S. Roos,, G. I. McFadden,, L. M. Cummings,, C. Mungall,, A. A. Kanapin,, J. C. Venter,, D. J. Carucci,, S. L. Hoffman,, C. Newbold,, R.W. Davis,, C. M. Fraser,, and B. Barrell. 2002. The genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498 511.
17. Hall, N.,, M. Karras,, J.D. Raine,, J.M. Carlton,,T.W. Kooij,, M. Berriman,, L. Florens,, C. S. Janssen,, A. Pain,, G. K. Christophides,, K. James,, K. Rutherford,, B. Harris,, D. Harris,, C. Churcher,, M. A. Quail,, D. Ormond,, J. Doggett,, H. E. Trueman,, J. Mendoza,, S. L. Bidwell,, M. A. Rajandream,, D. J. Carucci,, J. R. Yates,, F. C. Kafatos,, C. J. Janse,, B. Barrell,, C. M. Turner,, A. P. Waters,, and R. E. Sinden. 2005. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 307: 82 86.
18. Hiller, N. L.,, S. Bhattacharjee,, C. van Ooij,, K. Liolios,, T. Harrison,, C. L. Estrano,, and K. Haldar. 2004. A host-targeting signal in virulence proteins reveals a ‘secretome’ in malarial infection. Science 306: 1934 1937.
19. Johnson, R. S.,, and J.A. Taylor. 2002. Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol. Biotechnol . 22: 301 315.
20. Kaiser, K.,, K. Matuschewski,, N. Camargo,, J. Ross,, and S. H. Kappe. 2004. Transcriptome profiling identifies Plasmodium genes encoding pre-erythrocytic stage-specific proteins. Mol. Microbiol . 51: 1221 1232.
21. Kissinger, J. C.,, B. P. Brunk,, J. Crabtree,, M. J. Fraunholz,, B. Gajria,, A. J. Milgram,, D. S. Pearson,, J. Schug,, A. Bahl,, S. J. Diskin,, H. Ginsburg,, G. R. Grant,, D. Gupta,, P. Labo,, L. Li,, M. D. Mailman,, S. K. McWeeney,, P. Whetzel,, C. J. Stoeckert, Jr.,, and D. S. Roos. 2002. The Plasmodium genome database: designing and mining a eukaryotic genomics resource. Nature 419: 490 492.
22. Kissinger, J. C.,, and D. S. Roos,. 2004. Getting the most out of bioinformatics resources. In A. P. Waters, and C. J. Janse (ed.), Malaria Parasites. Horizon, Norfolk, United Kingdom.
23. Lasonder, E.,, Y. Ishihama,, J. S. Andersen,, A. M. Vermunt,, A. Pain,, R. W. Sauerwein,, W. M. Eling,, N, Hall,, A. P. Waters,, H. G. Stunnenberg,, and M. Man. 2002. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419: 537 542.
24. Le Roch,, K. G.,, Y. Zhou,, P. L. Blair,, M. Grainger,, J. K. Moch,, J. D. Haynes,, P. De la Vega,, A. A. Holder,, S. Batalov,, D. J. Carucci,, and E. A. Winzeler. 2003. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301: 1503 1508.
25. Le Roch, K. G.,, J. R. Johnson,, L. Florens,, Y. Zhou,, A. Santrosyan,, M. Grainger,, S. F. Yan,, K. C. Williamson,, A. A. Holder,, D. J. Carucci,, J. R. Yates,, and E. A. Winzeler. 2004. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 11: 2308 2318.
26. Li, L.,,C. J. Stoeckert, Jr.,, and D. S. Roos. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13: 2178 2190.
27. Li, L.,, J. Crabtree,, S. Fischer,, D. Pinney,, C. J. Stoeckert, Jr.,, L. D. Sibley,, and D. S. Roos. 2004. ApiESTDB: analyzing clustered EST data of the apicomplexan parasites. Nucleic Acids Res. 32: 326 328.
28. Mamoun, C. B.,, I. Y. Gluzman,, C. Hott,, S. K. MacMillan,, A. S. Amarkone,, D. L. Anderson,, J. M. Carlton,, J. B. Dame,, D. Chakrabarti,, R. K. Martin,, B. H. Brownstein,, and D. E. Goldberg. 2001. Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis. Mol. Microbiol . 39: 26 36.
29. Marti, M.,, R. T. Good,, M. Rug,, E. Knuepfer,, and A. F. Cowman. 2004. A unique export signal targets virulence and remodeling proteins from the malaria parasite to the host erythrocyte. Science 306: 1930 1933.
30. McGuffin, L. J.,, K. Bryson,, and D.T. ,surname . 2000. The PsiPred protein structure prediction server. Bioinformatics 16: 404–405.
31. Milgram, A. J.,, J. C. Kissinger,, B. Gajria,, D. S. Pearson,, A. Bahl,, P. Labo,, and D. S. Roos. 2003. Plasmodium falciparum GenePlot: Internet-independent access to the malaria parasite genome. Nature 422: CD–ROM. Distributed with the 6 March issue.
32. Pellegrini, M.,, E. M. Marcotte,, M. J.Thompson,, D. Eisenberg,, and T. O. Yeates. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96: 4285 4288.
33. Plasmodium Genome Database Collaborative. 2001. PlasmoDB: an integrative database of the Plasmodium falciparum genome.Tools for accessing and analyzing finished and unfinished sequence data. Nucleic Acids Res. 29: 6669.
34. Plotkin, J. B.,, J. Dushoff,, and H. B. Fraser. 2004. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature 428: 942 945.
35. Ralph, S. A.,, G. G. van Dooren,, R. F. Waller,, M. J. Crawford,, M. J. Fraunholz,, B. J. Foth,, C. J. Tonkin,, D. S. Roos,, and G. I. McFadden. 2004. Metabolic pathway maps and functions of the Plasmodium falciparum apicoplast. Nat. Rev. Microbiol . 2: 203 216.
36. Roos, D. S.,, M. J. Crawford,, R. G. K. Donald,, M. Fraunholz,, O. S. Harb,, C.Y. He,, J.C. Kissinger,, M. K. Shaw,, and B. Striepen. 2002. Mining the Plasmodium genome database to define organellar function: what does the apicoplast do? Phil.Trans.R. Soc. Lond. B Biol. Sci. 357: 35 46.
37. Sam-Yellowe, T.Y.,, L. Florens,, T. Wang,, J.D. Raine,, D. J. Carucci,, R. Sinden,, and J. R. Yates. 2004. Proteome analysis of rhoptry-enriched fractions isolated from Plasmodium merozoites. J. Proteome Res. 3: 995 1001.
38. Schuler, G.D. 1997. Sequence mapping by electronic PCR. Genome Res. 7: 541 550.
39. Servant, F.,, C. Bru,, S. Carrere,, E. Courcelle,, J. Gouzy,, D. Peyruc,, and D. Kahn. 2002. ProDom: automated clustering of homologous domains. Brief. Bioinformatics 3: 246 251.
40. Tongren, J. E.,, F. Zavala,, D. S. Roos,, and E. M. Riley. 2004. Malaria vaccines: if at first you don't succeed. . . . Trends Parasitol . 20: 604 610.
41. Zhou, Y.,, J. A. Young,, A. Santrosyan,, K. Chen,, F. S. Yan,, and E.A. Winzeler. 2005. In silico gene function prediction using ontology-based pattern identification. Bioinformatics 21: 1237 1245.

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