EuPathDB: the eukaryotic pathogen genomics database resource

被引：58

作者：

Aurrecoechea, Cristina ^{[1
]}

Barreto, Ana ^{[2
,3
]}

Basenko, Evelina Y. ^{[1
]}

Brestelli, John ^{[2
,3
]}

Brunk, Brian P. ^{[2
,4
]}

Cade, Shon ^{[4
]}

Crouch, Kathryn ^{[5
]}

Doherty, Ryan ^{[2
,4
]}

Falke, Dave ^{[1
]}

Fischer, Steve ^{[2
,3
]}

Gajria, Bindu ^{[2
,4
]}

Harb, Omar S. ^{[2
,4
]}

Heiges, Mark ^{[1
]}

Hertz-Fowler, Christiane ^{[6
]}

Hu, Sufen ^{[2
,4
]}

Iodice, John ^{[2
,3
]}

Kissinger, Jessica C. ^{[1
,7
,8
]}

Lawrence, Cris ^{[2
,4
]}

Li, Wei ^{[2
,4
]}

Pinney, Deborah F. ^{[2
,3
]}

Pulman, Jane A.

Roos, David S. ^{[4
]}

Shanmugasundram, Achchuthan ^{[9
]}

Silva-Franco, Fatima ^{[9
]}

Steinbiss, Sascha ^{[10
]}

Stoeckert, Christian J., Jr. ^{[2
,3
]}

Spruill, Drew

Wang, Haiming ^{[1
]}

Warrenfeltz, Susanne ^{[1
]}

Zheng, Jie ^{[2
,3
]}

机构：

[1] Univ Georgia, Ctr Trop & Emerging Global Dis, Athens, GA 30602 USA

[2] Univ Penn, Inst Biomed Informat, Perelman Sch Med, Philadelphia, PA 19104 USA

[3] Univ Penn, Dept Genet, Sch Med, Philadelphia, PA 19104 USA

[4] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA

[5] Univ Glasgow, Wellcome Trust Ctr Mol Parasitol, Glasgow G12 8TA, Lanark, Scotland

[6] Univ Liverpool, Ctr Genom Res, Liverpool L69 7ZB, Merseyside, England

[7] Univ Georgia, Dept Genet, Athens, GA 30602 USA

[8] Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA

[9] Univ Liverpool, Inst Integrat Biol, Ctr Genom Res, Liverpool L69 7ZB, Merseyside, England

[10] Wellcome Trust Sanger Inst, Parasite Genom, Wellcome Trust Genome Campus, Hinxton CB10 1SA, England

来源：

NUCLEIC ACIDS RESEARCH | 2017年 / 45卷 / D1期

基金：

美国国家卫生研究院; 英国惠康基金;

关键词：

BIOCHEMICAL PATHWAYS DATABASE; PLASMODIUM-FALCIPARUM; BIOINFORMATICS DATABASE; MALARIA; GENE; ENHANCEMENTS; EXPRESSION; ONTOLOGY; SILAC;

D O I：

10.1093/nar/gkw1105

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host-pathogen interactions.

引用

页码：D581 / D591

页数：11

共 35 条

[1]

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update [J].

Afgan, Enis ;

Baker, Dannon ;

van den Beek, Marius ;

Blankenberg, Daniel ;

Bouvier, Dave ;

Cech, Martin ;

Chilton, John ;

Clements, Dave ;

Coraor, Nate ;

Eberhard, Carl ;

Gruening, Bjoern ;

Guerler, Aysam ;

Hillman-Jackson, Jennifer ;

Von Kuster, Greg ;

Rasche, Eric ;

Soranzo, Nicola ;

Turaga, Nitesh ;

Taylor, James ;

Nekrutenko, Anton ;

Goecks, Jeremy .

NUCLEIC ACIDS RESEARCH, 2016, 44 (W1) :W3-W10

[2]

Differential expression analysis for sequence count data [J].

Anders, Simon ;

Huber, Wolfgang .

GENOME BIOLOGY, 2010, 11 (10)

[3]

HTSeq-a Python']Python framework to work with high-throughput sequencing data [J].

Anders, Simon ;

Pyl, Paul Theodor ;

Huber, Wolfgang .

BIOINFORMATICS, 2015, 31 (02) :166-169

[4]

EuPathDB: The Eukaryotic Pathogen database [J].

Aurrecoechea, Cristina ;

Barreto, Ana ;

Brestelli, John ;

Brunk, Brian P. ;

Cade, Shon ;

Doherty, Ryan ;

Fischer, Steve ;

Gajria, Bindu ;

Gao, Xin ;

Gingle, Alan ;

Grant, Greg ;

Harb, Omar S. ;

Heiges, Mark ;

Hu, Sufen ;

Iodice, John ;

Kissinger, Jessica C. ;

Kraemer, Eileen T. ;

Li, Wei ;

Pinney, Deborah F. ;

Pitts, Brian ;

Roos, David S. ;

Srinivasamoorthy, Ganesh ;

Stoeckert, Christian J., Jr. ;

Wang, Haiming ;

Warrenfeltz, Susanne .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D684-D691

[5]

Submicroscopic and asymptomatic Plasmodium falciparum and Plasmodium vivax infections are common in western Thailand - molecular and serological evidence [J].

Baum, Elisabeth ;

Sattabongkot, Jetsumon ;

Sirichaisinthop, Jeeraphat ;

Kiattibutr, Kirakorn ;

Davies, D. Huw ;

Jain, Aarti ;

Lo, Eugenia ;

Lee, Ming-Chieh ;

Randall, Arlo Z. ;

Molina, Douglas M. ;

Liang, Xiaowu ;

Cui, Liwang ;

Felgner, Philip L. ;

Yan, Guiyun .

MALARIA JOURNAL, 2015, 14

[6]

Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum [J].

Bunnik, Evelien M. ;

Chung, Duk-Won Doug ;

Hamilton, Michael ;

Ponts, Nadia ;

Saraf, Anita ;

Prudhomme, Jacques ;

Florens, Laurence ;

Le Roch, Karine G. .

GENOME BIOLOGY, 2013, 14 (11)

[7]

Caro F., 2014, eLife, pe04106

[8]

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases [J].

Caspi, Ron ;

Billington, Richard ;

Ferrer, Luciana ;

Foerster, Hartmut ;

Fulcher, Carol A. ;

Keseler, Ingrid M. ;

Kothari, Anamika ;

Krummenacker, Markus ;

Latendresse, Mario ;

Mueller, Lukas A. ;

Ong, Quang ;

Paley, Suzanne ;

Subhraveti, Pallavi ;

Weaver, Daniel S. ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D471-D480

[9]

Quantitative proteomics using SILAC: Principles, applications, and developments [J].

Chen, Xiulan ;

Wei, Shasha ;

Ji, Yanlong ;

Guo, Xiaojing ;

Yang, Fuquan .

PROTEOMICS, 2015, 15 (18) :3175-3192

[10]

A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray [J].

Crompton, Peter D. ;

Kayala, Matthew A. ;

Traore, Boubacar ;

Kayentao, Kassoum ;

Ongoiba, Aissata ;

Weiss, Greta E. ;

Molina, Douglas M. ;

Burk, Chad R. ;

Waisberg, Michael ;

Jasinskas, Algis ;

Tan, Xiaolin ;

Doumbo, Safiatou ;

Doumtabe, Didier ;

Kone, Younoussou ;

Narum, David L. ;

Liang, Xiaowu ;

Doumbo, Ogobara K. ;

Miller, Louis H. ;

Doolan, Denise L. ;

Baldi, Pierre ;

Felgner, Philip L. ;

Pierce, Susan K. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (15) :6958-6963

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