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Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data.

ABSTRACT: The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well as processing pipelines and analysis tools. Gene Ontology (GO, geneontology.org) is a major resource for gene enrichment analysis. The aim of this project, funded by the Alzheimer's Research United Kingdom (ARUK) foundation and led by the University College London (UCL) biocuration team, was to enhance the GO resource by developing new neurological GO terms, and use GO terms to annotate gene products associated with dementia. Specifically, proteins and protein complexes relevant to processes involving amyloid-beta and tau have been annotated and the resulting annotations are denoted in GO databases as 'ARUK-UCL'. Biological knowledge presented in the scientific literature was captured through the association of GO terms with dementia-relevant protein records; GO itself was revised, and new GO terms were added. This literature biocuration increased the number of Alzheimer's-relevant gene products that were being associated with neurological GO terms, such as 'amyloid-beta clearance' or 'learning or memory', as well as neuronal structures and their compartments. Of the total 2055 annotations that we contributed for the prioritised gene products, 526 have associated proteins and complexes with neurological GO terms. To ensure that these descriptive annotations could be provided for Alzheimer's-relevant gene products, over 70 new GO terms were created. Here, we describe how the improvements in ontology development and biocuration resulting from this initiative can benefit the scientific community and enhance the interpretation of dementia data.

SUBMITTER: Kramarz B

PROVIDER: S-EPMC6315915 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:EQ-5D is generic measure of health-related quality of life. Studies using EQ-5D generate ordinal data that are interpreted as categories ordered by severity. New analytic approaches taking into account the ordinal nature of the health dimension severity and leading to a better interpretation of EQ-5D data are needed to better elucidate differences in health-related quality of life. We propose utilizing the Improved RIDIT statistical method to analyze EQ-5D outcomes. METHODS:556 Moroccan participants aged over 18 years representing four chronic diseases: back pain (n = 158), renal insufficiency (n = 56), diabetes (n = 82) or hypertension (n = 80) and healthy subjects (n = 180). All participants received the two EQ-5D versions. Two other published data sets were included. The first was extracted from a diabetic Spain study and the second was extracted from a clinical trial study. The Improved RIDIT analyses were carried out using an R statistic program we developed. RESULTS:Applying the Improved RIDIT on the EQ-5D data allowed estimating for the first time the ordinal odds, the Absolute Risk Reduction (ARR) or the Absolute Risk Increase (ARI) and the Number Needed to Treat. The ARI values estimated for Moroccan patients showed that (i) hypertension increased anxiety/depression by 66% and reduced mobility by 65%; (ii) back pain increased pain/discomfort by 69%; (iii) renal insufficiency impacts mobility (ARI = 57%, oddsordinal = 9.95) and usual activities (ARI = 44%, oddsordinal = 6.41) and (iv) diabetes acts only on anxiety/depression (ARI = 50%, oddsordinal = 4.8). Also, we demonstrated that the approach works well in clinical trials. CONCLUSIONS:Improved RIDIT provides more intuitive and informative interpretation of the EQ-5D data by (1) taking into account the level severity; estimating (2) the odds ordinal, (3) the ARR/ARI and the NNT; (4) analyzing the five dimensions of the EQ-5D separately, which gives clinical teams more precision in understanding the treatment/pathology impacts on the health status and completes the EQ-5D data analysis based on score utilities.

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Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data.

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