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The Pathogen-Host Interactions database (PHI-base): additions and future developments.

Urban M, Pant R, Raghunath A, Irvine AG, Pedro H, Hammond-Kosack KE - Nucleic Acids Res. (2014)

Bottom Line: The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens.Mutant phenotypes are associated with gene information.PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK martin.urban@rothamsted.ac.uk.

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Related in: MedlinePlus

Inspection of gene function using the Ensembl genome browser. (A) Displayed is a small chromosomal region in Magnaporthe oryzae showing two genes involved in pathogenicity (as annotated in PHI-base) in their genomic context (viewable in the Ensembl browser, in the transcript display). A colour code indicates the annotated role of each gene, green ‘loss of pathogenicity’ and orange ‘reduced virulence’. (B) By selecting each colour-coded MGG transcript ID, information is revealed on the associated gene deletion study curated in the PHI-base database.
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Figure 3: Inspection of gene function using the Ensembl genome browser. (A) Displayed is a small chromosomal region in Magnaporthe oryzae showing two genes involved in pathogenicity (as annotated in PHI-base) in their genomic context (viewable in the Ensembl browser, in the transcript display). A colour code indicates the annotated role of each gene, green ‘loss of pathogenicity’ and orange ‘reduced virulence’. (B) By selecting each colour-coded MGG transcript ID, information is revealed on the associated gene deletion study curated in the PHI-base database.

Mentions: Through the cross-referencing with Ensembl Genomes (http://ensemblgenomes.org) PHI-base annotations can now be visualized directly in their genomic context, identifying features, such as pathogenicity islands through a simple system of colour coding using the nine high-level phenotyping terms. This new way to explore the data in PHI-base is shown in Figure 3. The phenotyping term ‘mixed outcome’ is also used to identify genes where a range of interaction outcomes have been identified depending on the host species and/or tissue type evaluated.


The Pathogen-Host Interactions database (PHI-base): additions and future developments.

Urban M, Pant R, Raghunath A, Irvine AG, Pedro H, Hammond-Kosack KE - Nucleic Acids Res. (2014)

Inspection of gene function using the Ensembl genome browser. (A) Displayed is a small chromosomal region in Magnaporthe oryzae showing two genes involved in pathogenicity (as annotated in PHI-base) in their genomic context (viewable in the Ensembl browser, in the transcript display). A colour code indicates the annotated role of each gene, green ‘loss of pathogenicity’ and orange ‘reduced virulence’. (B) By selecting each colour-coded MGG transcript ID, information is revealed on the associated gene deletion study curated in the PHI-base database.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383963&req=5

Figure 3: Inspection of gene function using the Ensembl genome browser. (A) Displayed is a small chromosomal region in Magnaporthe oryzae showing two genes involved in pathogenicity (as annotated in PHI-base) in their genomic context (viewable in the Ensembl browser, in the transcript display). A colour code indicates the annotated role of each gene, green ‘loss of pathogenicity’ and orange ‘reduced virulence’. (B) By selecting each colour-coded MGG transcript ID, information is revealed on the associated gene deletion study curated in the PHI-base database.
Mentions: Through the cross-referencing with Ensembl Genomes (http://ensemblgenomes.org) PHI-base annotations can now be visualized directly in their genomic context, identifying features, such as pathogenicity islands through a simple system of colour coding using the nine high-level phenotyping terms. This new way to explore the data in PHI-base is shown in Figure 3. The phenotyping term ‘mixed outcome’ is also used to identify genes where a range of interaction outcomes have been identified depending on the host species and/or tissue type evaluated.

Bottom Line: The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens.Mutant phenotypes are associated with gene information.PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK martin.urban@rothamsted.ac.uk.

Show MeSH
Related in: MedlinePlus