ArticleNucleic acids research2018
IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 33 citations in OpenAlex.
- AKR1C2 and AKR1C3 expression in adipose tissue: Association with body fat distribution and regulatory variants.Molecular and cellular endocrinology · 2021Trial
- MetaboGraph: A Framework for Metabolomics and Lipidomics Annotation and Pathway Network Analysis.Analytical chemistry · 2026Article
- Identification and functional characterization of regulatory variants in DPP9 associated with COVID-19 severity.Genome medicine · 2026Article
- Comparative genomic analysis of hypervirulent and classical Klebsiella pneumoniae isolates from respiratory samples: A computational assessment of virulence genes.Functional & integrative genomics · 2026Article
- Advancing genome-based precision medicine: a review on machine learning applications for rare genetic disorders.Briefings in bioinformatics · 2025Review
- Comprehensive assessment of computational methods for cancer immunoediting.Cell reports methods · 2025Article
- From Genome-wide Association Studies to Functional Variants: ARL14 Cis-regulatory Variants Are Associated With Severe Malaria.The Journal of infectious diseases · 2024Article
- RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants.Genomics, proteomics & bioinformatics · 2023Article
- Exploration of Tools for the Interpretation of Human Non-Coding Variants.International journal of molecular sciences · 2022Review
- Identification ofInternational journal of molecular sciences · 2022Article
- WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.Briefings in bioinformatics · 2021Article
- Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of aInternational journal of molecular sciences · 2021Article
- Enhancer-associated aortic valve stenosis risk locus 1p21.2 alters NFATC2 binding site and promotes fibrogenesis.iScience · 2021Article
- Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits.Scientific reports · 2020Article
- Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs.JCI insight · 2020Article
- Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.American journal of human genetics · 2020Article
- Cell Type-Specific Annotation and Fine Mapping of Variants Associated With Brain Disorders.Frontiers in genetics · 2020Article
- regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants.Nucleic acids research · 2019Article
- TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes.Nucleic acids research · 2019Article
- The Identification and Interpretation ofHigh-throughput · 2018Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The vast majority of germline and somatic variations occur in the noncoding part of the genome, only a small fraction of which are believed to be functional. From the tens of thousands of noncoding variations detectable in each genome, identifying and prioritizing driver candidates with putative functional significance is challenging. To address this, we implemented IW-Scoring, a new Integrative Weighted Scoring model to annotate and prioritise functionally relevant noncoding variations. We evaluate 11 scoring methods, and apply an unsupervised spectral approach for subsequent selective integration into two linear weighted functional scoring schemas for known and novel variations. IW-Scoring produces stable high-quality performance as the best predictors for three independent data sets. We demonstrate the robustness of IW-Scoring in identifying recurrent functional mutations in the TERT promoter, as well as disease SNPs in proximity to consensus motifs and with gene regulatory effects. Using follicular lymphoma as a paradigmatic cancer model, we apply IW-Scoring to locate 11 recurrently mutated noncoding regions in 14 follicular lymphoma genomes, and validate 9 of these regions in an extension cohort, including the promoter and enhancer regions of PAX5. Overall, IW-Scoring demonstrates greater versatility in identifying trait- and disease-associated noncoding variants. Scores from IW-Scoring as well as other methods are freely available from http://www.snp-nexus.org/IW-Scoring/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.