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IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis.

ABSTRACT: Improved bioassays have significantly increased the rate of identifying new protein-protein interactions (PPIs), and the number of detected human PPIs has greatly exceeded early estimates of human interactome size. These new PPIs provide a more complete view of disease mechanisms but precise understanding of how PPIs affect phenotype remains a challenge. It requires knowledge of PPI context (e.g. tissues, subcellular localizations), and functional roles, especially within pathways and protein complexes. The previous IID release focused on PPI context, providing networks with comprehensive tissue, disease, cellular localization, and druggability annotations. The current update adds developmental stages to the available contexts, and provides a way of assigning context to PPIs that could not be previously annotated due to insufficient data or incompatibility with available context categories (e.g. interactions between membrane and cytoplasmic proteins). This update also annotates PPIs with conservation across species, directionality in pathways, membership in large complexes, interaction stability (i.e. stable or transient), and mutation effects. Enrichment analysis is now available for all annotations, and includes multiple options; for example, context annotations can be analyzed with respect to PPIs or network proteins. In addition to tabular view or download, IID provides online network visualization. This update is available at http://ophid.utoronto.ca/iid.

SUBMITTER: Kotlyar M

PROVIDER: S-EPMC8728267 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Monitoring universal health coverage (UHC) focuses on information on health intervention coverage and financial protection. This paper addresses monitoring intervention coverage, related to the full spectrum of UHC, including health promotion and disease prevention, treatment, rehabilitation, and palliation. A comprehensive core set of indicators most relevant to the country situation should be monitored on a regular basis as part of health progress and systems performance assessment for all countries. UHC monitoring should be embedded in a broad results framework for the country health system, but focus on indicators related to the coverage of interventions that most directly reflect the results of UHC investments and strategies in each country. A set of tracer coverage indicators can be selected, divided into two groups-promotion/prevention, and treatment/care-as illustrated in this paper. Disaggregation of the indicators by the main equity stratifiers is critical to monitor progress in all population groups. Targets need to be set in accordance with baselines, historical rate of progress, and measurement considerations. Critical measurement gaps also exist, especially for treatment indicators, covering issues such as mental health, injuries, chronic conditions, surgical interventions, rehabilitation, and palliation. Consequently, further research and proxy indicators need to be used in the interim. Ideally, indicators should include a quality of intervention dimension. For some interventions, use of a single indicator is feasible, such as management of hypertension; but in many areas additional indicators are needed to capture quality of service provision. The monitoring of UHC has significant implications for health information systems. Major data gaps will need to be filled. At a minimum, countries will need to administer regular household health surveys with biological and clinical data collection. Countries will also need to improve the production of reliable, comprehensive, and timely health facility data. Please see later in the article for the Editors' Summary.

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IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis.

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