ArticleGenome research2010
Human genetic variation recognizes functional elements in noncoding sequence.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed, 67 citations in OpenAlex.
- Global assessment of genetic variation influencing response to retinoid chemoprevention in head and neck cancer patients.Cancer prevention research (Philadelphia, Pa.) · 2011Trial
- Genetic variants inHeliyon · 2024Article
- Enhancer-promoter activation by the Kaposi sarcoma-associated herpesvirus episome maintenance protein LANA.Cell reports · 2024Article
- Fyn and Lyn gene polymorphisms impact the risk of thyroid cancer.Molecular genetics and genomics : MGG · 2022Article
- A Post-GWAS Functional Analysis Confirming Effects of Three BTA13 GenesFrontiers in genetics · 2022Article
- Genetic Variations in Prostaglandin EInternational journal of molecular sciences · 2021Article
- Association of intronic polymorphisms (rs1549339, rs13402242) and mRNA expression variations in PSMD1 gene in arsenic-exposed workers.Environmental science and pollution research international · 2020Article
- SNP Diversity inGenes · 2020Article
- Molecular Imaging of Opioid and Dopamine Systems: Insights Into the Pharmacogenetics of Opioid Use Disorders.Frontiers in psychiatry · 2019Review
- Epigenetic modifications inClinical epigenetics · 2018Article
- Haplotype analysis of XRCC2 gene polymorphisms and association with increased risk of head and neck cancer.Scientific reports · 2017Article
- Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq.Molecules and cells · 2017Article
- Genomic strategies to understand causes of keratoconus.Molecular genetics and genomics : MGG · 2017Review
- Genomic translational research: Paving the way to individualized cardiac functional analyses and personalized cardiology.International journal of cardiology · 2017Review
- Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis.Advances and applications in bioinformatics and chemistry : AABC · 2017Article
- Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer.Cell reports · 2016Article
- Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.Nature genetics · 2016Article
- A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events.PLoS computational biology · 2015Article
- Weak negative and positive selection and the drift load at splice sites.Genome biology and evolution · 2014Article
- HPA axis genetic variation, cortisol and psychosis in major depression.Molecular psychiatry · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Noncoding DNA, particularly intronic DNA, harbors important functional elements that affect gene expression and RNA splicing. Yet, it is unclear which specific noncoding sites are essential for gene function and regulation. To identify functional elements in noncoding DNA, we characterized genetic variation within introns using ethnically diverse human polymorphism data from three public databases-PMT, NIEHS, and SeattleSNPs. We demonstrate that positions within introns corresponding to known functional elements involved in pre-mRNA splicing, including the branch site, splice sites, and polypyrimidine tract show reduced levels of genetic variation. Additionally, we observed regions of reduced genetic variation that are candidates for distance-dependent localization sites of functional elements, possibly intronic splicing enhancers (ISEs). Using several bioinformatics approaches, we provide additional evidence that supports our hypotheses that these regions correspond to ISEs. We conclude that studies of genetic variation can successfully discriminate and identify functional elements in noncoding regions. As more noncoding sequence data become available, the methods employed here can be utilized to identify additional functional elements in the human genome and provide possible explanations for phenotypic associations.
Indexed as
Identifiers
What OpenQuestion holds
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.