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Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, Sahu J, Iyer SV, Khamari L, De Silva N, Martinez MC, Pedro H, Yates AD, Hammond-Kosack KE. PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. Nucleic Acids Res 2021; 50:D837-D847. [PMID: 34788826 PMCID: PMC8728202 DOI: 10.1093/nar/gkab1037] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 12/28/2022] Open
Abstract
Since 2005, the Pathogen–Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.
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Affiliation(s)
- Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Alayne Cuzick
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - James Seager
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Valerie Wood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Kim Rutherford
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Jashobanta Sahu
- Molecular Connections, Kandala Mansions, Kariappa Road, Basavanagudi, Bengaluru 560 004, India
| | - S Vijaylakshmi Iyer
- Molecular Connections, Kandala Mansions, Kariappa Road, Basavanagudi, Bengaluru 560 004, India
| | - Lokanath Khamari
- Molecular Connections, Kandala Mansions, Kariappa Road, Basavanagudi, Bengaluru 560 004, India
| | - Nishadi De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Carbajo Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helder Pedro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK
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Schaffer LV, Ideker T. Mapping the multiscale structure of biological systems. Cell Syst 2021; 12:622-635. [PMID: 34139169 PMCID: PMC8245186 DOI: 10.1016/j.cels.2021.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/04/2021] [Accepted: 05/14/2021] [Indexed: 01/14/2023]
Abstract
Biological systems are by nature multiscale, consisting of subsystems that factor into progressively smaller units in a deeply hierarchical structure. At any level of the hierarchy, an ever-increasing diversity of technologies can be applied to characterize the corresponding biological units and their relations, resulting in large networks of physical or functional proximities-e.g., proximities of amino acids within a protein, of proteins within a complex, or of cell types within a tissue. Here, we review general concepts and progress in using network proximity measures as a basis for creation of multiscale hierarchical maps of biological systems. We discuss the functionalization of these maps to create predictive models, including those useful in translation of genotype to phenotype, along with strategies for model visualization and challenges faced by multiscale modeling in the near future. Collectively, these approaches enable a unified hierarchical approach to biological data, with application from the molecular to the macroscopic.
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Affiliation(s)
- Leah V Schaffer
- Division of Genetics, Department of Medicine, University of California San Diego, San Diego, La Jolla, CA 92093, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, San Diego, La Jolla, CA 92093, USA.
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Thomas G, Bain JM, Budge S, Brown AJP, Ames RM. Identifying Candida albicans Gene Networks Involved in Pathogenicity. Front Genet 2020; 11:375. [PMID: 32391057 PMCID: PMC7193023 DOI: 10.3389/fgene.2020.00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/26/2020] [Indexed: 11/17/2022] Open
Abstract
Candida albicans is a normal member of the human microbiome. It is also an opportunistic pathogen, which can cause life-threatening systemic infections in severely immunocompromized individuals. Despite the availability of antifungal drugs, mortality rates of systemic infections are high and new drugs are needed to overcome therapeutic challenges including the emergence of drug resistance. Targeting known disease pathways has been suggested as a promising avenue for the development of new antifungals. However, <30% of C. albicans genes are verified with experimental evidence of a gene product, and the full complement of genes involved in important disease processes is currently unknown. Tools to predict the function of partially or uncharacterized genes and generate testable hypotheses will, therefore, help to identify potential targets for new antifungal development. Here, we employ a network-extracted ontology to leverage publicly available transcriptomics data and identify potential candidate genes involved in disease processes. A subset of these genes has been phenotypically screened using available deletion strains and we present preliminary data that one candidate, PEP8, is involved in hyphal development and immune evasion. This work demonstrates the utility of network-extracted ontologies in predicting gene function to generate testable hypotheses that can be applied to pathogenic systems. This could represent a novel first step to identifying targets for new antifungal therapies.
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Affiliation(s)
- Graham Thomas
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Judith M Bain
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Susan Budge
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alistair J P Brown
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.,MRC Centre for Medical Mycology at the University of Exeter, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Ryan M Ames
- Biosciences, University of Exeter, Exeter, United Kingdom
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Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Syst 2019; 8:267-273.e3. [PMID: 30878356 PMCID: PMC7042149 DOI: 10.1016/j.cels.2019.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 12/08/2018] [Accepted: 02/08/2019] [Indexed: 01/08/2023]
Abstract
Systems biology requires not only genome-scale data but also methods to integrate these data into interpretable models. Previously, we developed approaches that organize omics data into a structured hierarchy of cellular components and pathways, called a "data-driven ontology." Such hierarchies recapitulate known cellular subsystems and discover new ones. To broadly facilitate this type of modeling, we report the development of a software library called the Data-Driven Ontology Toolkit (DDOT), consisting of a Python package (https://github.com/idekerlab/ddot) to assemble and analyze ontologies and a web application (http://hiview.ucsd.edu) to visualize them. Using DDOT, we programmatically assemble a compendium of ontologies for 652 diseases by integrating gene-disease mappings with a gene similarity network derived from omics data. For example, the ontology for Fanconi anemia describes known and novel disease mechanisms in its hierarchy of 194 genes and 74 subsystems. DDOT provides an easy interface to share ontologies online at the Network Data Exchange.
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Affiliation(s)
- Michael Ku Yu
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jianzhu Ma
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Keiichiro Ono
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fan Zheng
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samson H Fong
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aaron Gary
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jing Chen
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Barry Demchak
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dexter Pratt
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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Wang Z, Gudibanda A, Ugwuowo U, Trail F, Townsend JP. Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Genome-Wide Transcriptome Analysis Reveals the Comprehensive Response of Two Susceptible Poplar Sections to Marssonina brunnea Infection. Genes (Basel) 2018. [PMID: 29534547 PMCID: PMC5867875 DOI: 10.3390/genes9030154] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Marssonina leaf spot disease of poplar (MLDP), caused by the hemibiotrophic pathogen Marssonina brunnea, frequently results in damage to many poplar species. In nature, two formae speciales of M. brunnea exist that are susceptible to different poplar subgenera. Marssonina brunnea f. sp. monogermtubi infects poplar hosts from Populus sect. Aigeiros (Aig), while M. brunnea f. sp. multigermtubi always infects poplar hosts from Populus sect. Leuce Duby (Leu). Based on the fungal penetration structures, a comprehensive transcriptomic approach was used to investigate the gene expression patterns of these two poplar subgenera at three crucial infection stages. MLDP significantly altered the expression patterns of many genes involved in mitogen activated protein kinase (MAPKs) and calcium signaling, transcription factors, primary and secondary metabolism, and other processes in both poplar subgenera. However, major differences in gene expression were also observed between the two poplar subgenera. Aig was most responsive at the initial infection stage, while Leu largely interacted with M. brunnea at the necrotrophic phase. Furthermore, the differentially expressed genes (DEGs) involved in pathways related to biotic stress also differed substantially between the two poplar subgenera. Further analysis indicated that the genes involved in cell wall metabolism and phenylpropanoid metabolism were differentially expressed in the progression of the disease. By examining the expression patterns of genes related to the defense against disease, we found that several genes annotated with causing hypersensitive cell death were upregulated at the necrotrophic phase of MLDP, inferring that plant immune response potentially happened at this infection stage. The present research elucidated the potential molecular differences between the two susceptible interaction systems in MLDP and provided novel insight into the temporal regulation of genes during the susceptible response. To the best of our knowledge, this study also constitutes the first to reveal the molecular mechanisms of poplar in response to the transition of hemibiotrophic fungal pathogens from the biotrophic phase to the necrotrophic phase.
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