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EuPathDB: The Eukaryotic Pathogen Genomics Database Resource

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Eukaryotic Genomic Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1757))

Abstract

Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen’s biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources (http://eupathdb.org) are data mining resources that support hypothesis driven research by facilitating the discovery of meaningful biological relationships from large volumes of data. The resource encompasses 13 sites that support over 170 species including pathogenic protists, oomycetes, and fungi as well as evolutionarily related nonpathogenic species. EuPathDB integrates preanalyzed data with advanced search capabilities, data visualization, analysis tools and a comprehensive record system in a graphical interface that does not require prior computational skills. This chapter describes guiding concepts common across EuPathDB sites and illustrates the powerful data mining capabilities of some of the available tools and features.

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References

  1. Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, Hu S, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS, Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ Jr, Spruill D, Wang H, Warrenfeltz S, Zheng J (2017) EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res 45(D1):D581–D591. https://doi.org/10.1093/nar/gkw1105

    Article  PubMed  CAS  Google Scholar 

  2. Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Hu S, Iodice J, Kissinger JC, Kraemer ET, Li W, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Wang H, Warrenfeltz S (2013) EuPathDB: the eukaryotic pathogen database. Nucleic Acids Res 41(Database issue):D684–D691. https://doi.org/10.1093/nar/gks1113

    Article  PubMed  CAS  Google Scholar 

  3. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12(10):1599–1610

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C, Berriman M, Otto TD (2016) Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Res 44(W1):W29–W34. https://doi.org/10.1093/nar/gkw292

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Peng D, Tarleton R (2015) EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens. Microb Genom 1(4):e000033. https://doi.org/10.1099/mgen.0.000033

    Article  PubMed  PubMed Central  Google Scholar 

  6. Bunnik EM, Chung DW, Hamilton M, Ponts N, Saraf A, Prudhomme J, Florens L, Le Roch KG (2013) Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum. Genome Biol 14(11):R128. https://doi.org/10.1186/gb-2013-14-11-r128

    Article  PubMed  PubMed Central  Google Scholar 

  7. Lopez-Barragan MJ, Lemieux J, Quinones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K, XZ S (2011) Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. BMC Genomics 12:587. https://doi.org/10.1186/1471-2164-12-587

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Lasonder E, Green JL, Camarda G, Talabani H, Holder AA, Langsley G, Alano P (2012) The Plasmodium falciparum schizont phosphoproteome reveals extensive phosphatidylinositol and cAMP-protein kinase A signaling. J Proteome Res 11(11):5323–5337. https://doi.org/10.1021/pr300557m

    Article  PubMed  CAS  Google Scholar 

  9. Solyakov L, Halbert J, Alam MM, Semblat JP, Dorin-Semblat D, Reininger L, Bottrill AR, Mistry S, Abdi A, Fennell C, Holland Z, Demarta C, Bouza Y, Sicard A, Nivez MP, Eschenlauer S, Lama T, Thomas DC, Sharma P, Agarwal S, Kern S, Pradel G, Graciotti M, Tobin AB, Doerig C (2011) Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum. Nat Commun 2:565. https://doi.org/10.1038/ncomms1558

    Article  PubMed  CAS  Google Scholar 

  10. Oehring SC, Woodcroft BJ, Moes S, Wetzel J, Dietz O, Pulfer A, Dekiwadia C, Maeser P, Flueck C, Witmer K, Brancucci NM, Niederwieser I, Jenoe P, Ralph SA, Voss TS (2012) Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum. Genome Biol 13(11):R108. https://doi.org/10.1186/gb-2012-13-11-r108

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Dewey CN (2007) Aligning multiple whole genomes with Mercator and MAVID. Methods Mol Biol 395:221–236

    Article  CAS  PubMed  Google Scholar 

  12. Kanehisa M (2002) The KEGG database. Novartis Found Symp 247:91–101. discussion 101–103, 119–128, 244–152

    Article  CAS  PubMed  Google Scholar 

  13. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34(Database issue):D354–D357

    Article  CAS  PubMed  Google Scholar 

  14. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44(D1):D457–D462. https://doi.org/10.1093/nar/gkv1070

    Article  PubMed  CAS  Google Scholar 

  15. Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 44(D1):D471–D480. https://doi.org/10.1093/nar/gkv1164

    Article  PubMed  CAS  Google Scholar 

  16. Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Butikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Maser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F (2015) TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Res 43(Database issue):D637–D644. https://doi.org/10.1093/nar/gku944

    Article  PubMed  CAS  Google Scholar 

  17. Saunders EC, MacRae JI, Naderer T, Ng M, McConville MJ, Likic VA (2012) LeishCyc: a guide to building a metabolic pathway database and visualization of metabolomic data. Methods Mol Biol 881:505–529. https://doi.org/10.1007/978-1-61779-827-6_17

    Article  PubMed  CAS  Google Scholar 

  18. Doyle MA, MacRae JI, De Souza DP, Saunders EC, McConville MJ, Likic VA (2009) LeishCyc: a biochemical pathways database for Leishmania major. BMC Syst Biol 3:57. https://doi.org/10.1186/1752-0509-3-57

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD (2016) Cytoscape.js: a graph theory library for visualisation and analysis. Bioinformatics 32(2):309–311. https://doi.org/10.1093/bioinformatics/btv557

    Article  PubMed  CAS  Google Scholar 

  20. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T (2012) A travel guide to Cytoscape plugins. Nat Methods 9(11):1069–1076. https://doi.org/10.1038/nmeth.2212

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Siegel TN, Hekstra DR, Wang X, Dewell S, Cross GA (2010) Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites. Nucleic Acids Res 38(15):4946–4957. https://doi.org/10.1093/nar/gkq237

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Gene Ontology C (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res 43(Database issue):D1049–D1056. https://doi.org/10.1093/nar/gku1179

    Article  CAS  Google Scholar 

  25. Lasonder E, Rijpma SR, van Schaijk BC, Hoeijmakers WA, Kensche PR, Gresnigt MS, Italiaander A, Vos MW, Woestenenk R, Bousema T, Mair GR, Khan SM, Janse CJ, Bartfai R, Sauerwein RW (2016) Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression. Nucleic Acids Res 44(13):6087–6101. https://doi.org/10.1093/nar/gkw536

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztanyi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL (2017) InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45(D1):D190–D199. https://doi.org/10.1093/nar/gkw1107

    Article  PubMed  CAS  Google Scholar 

  27. Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Eberhard C, Gruning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J (2016) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 44(W1):W3–W10. https://doi.org/10.1093/nar/gkw343

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Liu B, Madduri RK, Sotomayor B, Chard K, Lacinski L, Dave UJ, Li J, Liu C, Foster IT (2014) Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses. J Biomed Inform 49:119–133. https://doi.org/10.1016/j.jbi.2014.01.005

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

EuPathDB would like to acknowledge their current funders, the National Institutes of Health (USA), the Wellcome Trust (UK), as well as past funders and The Bill and Melinda Gates Foundation (USA), The Burroughs Wellcome Fund (USA).

Author information

Authors and Affiliations

  1. Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA

    Susanne Warrenfeltz & Jessica C. Kissinger

  2. Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK

    Evelina Y. Basenko, Achchuthan Shanmugasundram & Fatima Silva-Franco

  3. Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, UK

    Kathryn Crouch

  4. Department of Biology, University of Pennsylvania, Philadelphia, PA, USA

    Omar S. Harb & David S. Roos

  5. Institute of Bioinformatics, University of Georgia, Athens, GA, USA

    Jessica C. Kissinger

  6. Department of Genetics, University of Georgia, Athens, GA, USA

    Jessica C. Kissinger

Authors
  1. Susanne Warrenfeltz
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  2. Evelina Y. Basenko
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  3. Kathryn Crouch
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  4. Omar S. Harb
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  5. Jessica C. Kissinger
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  6. David S. Roos
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  7. Achchuthan Shanmugasundram
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  8. Fatima Silva-Franco
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Corresponding author

Correspondence to Susanne Warrenfeltz .

Editor information

Editors and Affiliations

  1. Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

    Martin Kollmar

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Warrenfeltz, S. et al. (2018). EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. In: Kollmar, M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7737-6_5

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  • DOI: https://doi.org/10.1007/978-1-4939-7737-6_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7736-9

  • Online ISBN: 978-1-4939-7737-6

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