The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238852 | PMC |
| http://dx.doi.org/10.1093/nar/gkm858 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn's disease by bioinformatics analysis and machine learning.
Sci Rep
January 2025
General Surgery Department, Jiangsu University Affiliated People's Hospital, Zhenjiang, 212000, China.
Crohn's disease (CD) is a chronic inflammatory bowel disease with an unknown etiology. Ubiquitination plays a significant role in the pathogenesis of CD. This study aimed to explore the functional roles of ubiquitination-related genes in CD.
View Article and Find Full Text PDFASIC1a mediated nucleus pulposus cells pyroptosis and glycolytic crosstalk as a molecular basis for intervertebral disc degeneration.
Inflamm Res
January 2025
Department of Orthopedics and Traumatology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan Province, China.
Background: One of the etiologic components of degenerative spinal illnesses is intervertebral disc degeneration (IVDD), and the accompanying lower back pain is progressively turning into a significant public health problem. Important pathologic characteristics of IVDD include inflammation and acidic microenvironment, albeit it is unclear how these factors contribute to the disease.
Purpose: To clarify the functions of inflammation and the acidic environment in IVDD, identify the critical connections facilitating glycolytic crosstalk and nucleus pulposus cells (NPCs) pyroptosis, and offer novel approaches to IVDD prevention and therapy.
Exploring the Use of Smartwatches and Activity Trackers for Health-Related Purposes for Children Aged 5 to 11 years: Systematic Review.
J Med Internet Res
January 2025
University of Bristol, Bristol, United Kingdom.
Background: Digital health interventions targeting behavior change are promising in adults and adolescents; however, less attention has been given to younger children. The proliferation of wearables, such as smartwatches and activity trackers, that support the collection of and reflection on personal health data highlights an opportunity to consider novel approaches to supporting health in young children (aged 5-11 y).
Objective: This review aims to investigate how smartwatches and activity trackers have been used across child health interventions (for children aged 5-11 y) for different health areas, specifically to identify the population characteristics of those being targeted, describe the characteristics of the devices being used, and report the feasibility and acceptability of these devices for health-related applications with children.
LYVE1 and IL1RL1 are mitochondrial permeability transition-driven necrosis-related genes in heart failure.
Int J Biochem Cell Biol
January 2025
Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, China. Electronic address:
Background: Heart failure is linked to increased hospitalization and mortality. Mitochondrial permeability transition-driven necrosis is associated with cardiovascular diseases, but its role in heart failure is unclear. This study aimed to identify and validate genes related to mitochondrial permeability transition-driven necrosis in heart failure, potentially leading to new drug targets and signaling pathways.
View Article and Find Full Text PDFThe UnconTrust Database for Studies of Unconscious Semantic Processing and Attentional Allocation.
Sci Data
January 2025
School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel.
The question of what processes can take place without conscious awareness has generated extensive research. Yet there is still no consensus regarding the extent and scope of unconscious processing, and past research abounds with conflicting results. A possible reason for this lack of consensus is the diversity of methods in the field, as the methodological choices might influence the results.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!