Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies.
Catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. It proposes improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. PHI-base contains information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions.
Supplies a collection of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. VirHostNet simplifies systems biology and gene-centered analysis of infectious diseases and assists users in the recognition of new molecular targets for antiviral drugs design. It aims to improve the knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system.
Provides annotation for pathogen-host interaction (PHI)-related pathogen and host genes. Phigen gathers manually curated PHI gene information. Users can submit data for curation of pathogen genes, especially their roles in PHI. The curation focuses on adding PHI-related information, such as host immune responses, gene mutations and resultant pathogenic changes in the host. It can assist researchers in surveying, comparing, and studying gene-specific PHI mechanisms. Phigen is part of PHIDIAS.
Allows curation and visualization of pathogen-host interaction network. Phinet is a database that focuses on the analysis of molecular networks responsible for pathogen-host interactions. An internal graphviz-based visualization software permits displaying of all pathway data for each pathogen available in the resource. Internal or external curators can submit PHI-related network data. Phinet is part of PHIDIAS.
Gathers conserved domains of proteins from pathogen genomes analyzed in PHIDIAS. Pacodom is a pathogen-specific protein conserved domains database that stores more than 7900 position-specific scoring matrices (PSSM) found from more about 153160 protein sequences. It includes conserved domains from both pathogenic strains and nonpathogenic strains of the same microbial species. Pacodom is part of PHIDIAS.
Provides access to pathogen and pathogen-host interaction (PHI) information curated from biomedical literature or other curated data sources. Phinfo is a database containing more than 30 pathogens from about 2890 references. Users can perform keyword searches to query for specific pathogen and PHI information or topic searches. Phinfo is part of PHIDIAS.
Centralizes resources about several human or zoonotic priority pathogens, and focuses on searching, visualization, comparison, and analysis of pathogen genes and their interactions with their hosts. PHIDIAS is a web-based database and analysis system that includes six components that search and analyze annotated genome sequences, curated pathogen-host interaction (PHI) data, and PHI-related gene expression data. It also allows curators to submit annotated data for genes as well as genetic interactions and pathways.
A virus-virus and virus-host interaction resource build on the detailed curation protocols of the IMEx consortium and on the integration strategies developed for mentha. VirusMentha is regularly and automatically updated every week by capturing, via the PSICQUIC protocol, interactions curated by five different databases that are part of the IMEx consortium.
A manually curated database of interactions between host-pathogen-related elements such as biomolecules (proteins, metabolites etc.) and other factors (biological processes, cellular components etc.). HoPaCI-DB is an analysis resource for the study of the pathogens Pseudomonas aeruginosa and Coxiella species. The majority of host species refers to mammalia, but also results from experiments with C. elegans, Drosophila melanogaster or Danio rerio are included. The aim of HoPaCI-DB is to serve as knowledge base for experimentally- oriented scientists and as resource for bioinformatics applications.
Provides a database of known interactions of HIV-1 proteins with proteins from human hosts. HIV-1 Human Interaction Database is an online resource that includes annotated bibliographies of published reports of protein interactions, with links to the corresponding PubMed records and sequence data. It also integrates published reports of two types of interactions - protein interactions, and human gene knock-downs that affect virus replication and infectivity.
Gathers more than 260 pairs of mammalian virus-host receptor interaction. Viral Receptor organizes its collected data by viral species/sub-species and by virus receptors of 13 mammal species. This repository aims to underline the structural diversity of mammalian virus receptors. It intends to assist researchers to identify viral receptors via the study of structural, evolutionary and tissue-specific expression characteristics of mammalian virus receptors.
Facilitates both the identification and functional analysis of host–pathogen interactions (HPI) for a broad range of pathogens and their hosts. HPIDB 2.0 provides targeted curation, integration with existing HPI data from external sources and tool(s) to predict additional HPI where annotated data is scarce. This unique quality of HPIDB 2.0 ensures that researchers have access to the most comprehensive data set for their system and avoid the time-consuming series of steps required to integrate, standardize and annotate HPI data.
Provides pathogen–host interactions (PHIs) information. PHISTO is a web-accessible platform allowing to access to PHI data for all pathogen types. The database is updating each month in order to give access to users to up-to-date PHI data. It contains several functions which permit: (1) visualization of PHI network, (2) graph–theoretical analysis of targeted human proteins, (3) BLAST search and text mining for spotting new experimental methods.
Allows researchers and scientists to find knowledge and clinical solutions for disease mechanism understanding, diagnosis and therapy. HMDAD is a database based on microbiota studies in order to collect the human microbe-disease association data. The web interface of the database has a browse mode, a search mode, and permits users to download the dataset. It integrates more than 480 disease-microbe entries including about 30 diseases and 290 microbes.
Plants are continuously subjected to infection by pathogens, including bacteria and viruses. This present work is probably the first comprehensive study of constructing pathways that comprises effector, microRNA, target genes and PPI for the study of pathogen-host interactions. It is expected that this study may help to elucidate the role of pathogen-host interplay in a plant's immune system.
A database on protein-protein interactions between ralstonia solanacearum (a plant pathogen) and arabidopsis thaliana (its host). Using two computational methods, the interolog and the domain-based methods, we predicted 3,074 potential PPIs between 119 R. solanacearum and 1,442 A. thaliana proteins. Interestingly, we found that the potential pathogen-targeted proteins are more important in the A. thaliana PPI network.
Records, shares and provides access to data about E. multilocularis, focusing on the EmsB microsatellite. EWET-DB consists in a reference collection dedicated to Echinococcus genetic data. Users can consult isolate data (including EmsB data) and distribution map from the database using different criteria (host, country, province, year of sampling, etc.). The database also allows researchers to perform genetic and spatial analyses on the reference collection and their own data.
Provides functional Brucella gene information and analysis tools. BBP also enables users to (1) search for specific Brucella gene information and provide links to existing databases through the BBP InterBru database, and (2) obtain graphic visualization through the Brucella Genome Browser. The portal also focuses on annotating Brucella genes and gene-gene interactions from literature publications, and includes computational Brucella literature search tools for retrieving Brucella articles.
Domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Retreival of such vast information from different resources with a provision of prediction and validation of proteins structures would help researchers in designing the strain specific drugs/vaccines to prevail over the cancerous consequences.
Gathers network data (metabolic, regulatory, protein-protein interaction) for 10 representative pathogenic Salmonella strains. SalmoNet is an online database regrouping information on interactions from multiple layers of biological organization. This repository allows users to study pathogen Salmonella with details in a standardized and documented format. It can be applied by medical microbiologists and epidemiologists to understand the strain specific differences of Salmonella.