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Protocols

PHI-base specifications

Information


Unique identifier OMICS_07527
Name PHI-base
Alternative names Pathogen-Host Interactions database, PHIbase
Restrictions to use Academic or non-commercial use
Database management system NoSQL
Community driven Yes
Data access File download, Browse
User data submission Allowed
Version 4.2
Content license CC Attribution-NonCommercial-NoDerivs
Maintained Yes

Documentation


Maintainer


  • person_outline Martin Urban

Publications for Pathogen-Host Interactions database

PHI-base citations

 (77)
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The Fusarium graminearum Histone Acetyltransferases Are Important for Morphogenesis, DON Biosynthesis, and Pathogenicity

2018
Front Microbiol
PMCID: 5932188
PMID: 29755419
DOI: 10.3389/fmicb.2018.00654
call_split See protocol

[…] ism gene clusters were predicted by Sieber et al. (). Genes associated with sexual reproduction were from two previous reports (Hallen et al., ; Kim et al., ). Virulence-related genes were found from PHI-base database (http://www.phi-base.org/index.jsp). […]

library_books

Inter genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum

2018
BMC Genomics
PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] nenatum genome was compared to F. graminearum and seven other ascomycetes with highly contrasting lifestyles using protein domain signatures known to be functionally linked to virulence [] within the PHI-base gene set. The additional species selected were the floral maize pathogen F. verticillioides, the floral cereal pathogen F. langsethiae, the tomato root and vascular pathogen F. oxysporum f. s […]

library_books

Characterization of Heterobasidion occidentale transcriptomes reveals candidate genes and DNA polymorphisms for virulence variations

2018
PMCID: 5954486
PMID: 29611344
DOI: 10.1111/1751-7915.13259

[…] from the H. irregulare TC32‐1 reference genome by Blast analysis. In addition to the secretome identified in full‐length ORFs, other candidate effectors were revealed by Blast search against the PHI (pathogen–host interactions) database, which contained 4003 proteins (Urban et al., ). The dbCAN web server (HMMs 6.0) was used to identify putative CAZymes by searching against CAZyDB with default par […]

library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] onfirmed the absence of these two regions in the 14 isolates, excluding the chances of mis-assembly of reference genome (Additional file : Figure S7). Five out of 7 proteins in scaffold38 had hits in PHI-base with either “reduced virulence” or “loss of pathogenicity” annotations (Table ). On scaffold51, two secreted proteins with no functional annotation and one glucose-6-phosphate isomerase were […]

library_books

Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen

2018
PLoS One
PMCID: 5870968
PMID: 29584736
DOI: 10.1371/journal.pone.0194616

[…] se proteins were further explored using BLAST [] and CDD [,] database searches. We also identified secreted proteins that lacked a transmembrane domain using SignalP version 4.1 []. Blast searches of PHI-base (www.PHI-base.org) were also conducted to examine homology with functionally characterized virulence genes in F. graminearum and other phytopathogenic microbes.Gene Ontology (GO) enrichment a […]

library_books

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

2018
PMCID: 5872342
DOI: 10.3390/jof4010039

[…] nternal curation, or user-submitted data (user comments, see below).The Link outs section offers redirection to other resources including EnsemblFungi [], Entrez Gene [], FGSC [], UniProt [], JGI [], PHI-Base [], AspGD [], PhylomeDB [], PomBase [], CGD [], SGD [], and others.The Genomic Location section contains gene or sequence coordinates within a chromosome or contig/scaffold and a link out to […]

Citations

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PHI-base institution(s)
Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK; Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Sanger Building, Cambridge, UK; The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, UK; Molecular Connections Private Limited, Bangalore, India
PHI-base funding source(s)
UK Biotechnology and Biological Sciences Research Council (BBSRC) (BB/I/001077/1, BB/K020056/1), BBSRC as a National Capability (BB/J/004383/1).

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