ReviewCold Spring Harbor protocols2015
Using the ENCODE Resource for Functional Annotation of Genetic Variants.
Review in Cold Spring Harbor protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Serpin peptidase inhibitor (SERPINB5) haplotypes are associated with susceptibility to hepatocellular carcinoma.Scientific reports · 2016Trial
- Remote regulation of rs80245547 and rs72673891 mediated by transcription factors C-Jun and CREB1 affectiScience · 2023Article
- Identifying polymorphic cis-regulatory variants as risk markers for lung carcinogenesis and chemotherapy responses in tobacco smokers from eastern India.Scientific reports · 2023Article
- Molecular networks in Network Medicine: Development and applications.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- The contribution of rare genetic variants to the pathogenesis of polycystic ovary syndrome.Current opinion in endocrine and metabolic research · 2020Article
- Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.Genome biology · 2020Article
- Annot: a Django-based sample, reagent, and experiment metadata tracking system.BMC bioinformatics · 2019Article
- lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells.Scientific reports · 2019Article
- Clinical application of next-generation sequencing to the practice of neurology.The Lancet. Neurology · 2019Review
- A functional genetic variation of SLC6A2 repressor hsa-miR-579-3p upregulates sympathetic noradrenergic processes of fear and anxiety.Translational psychiatry · 2018Article
- Association of Novel ALX4 Gene Polymorphisms with Antidepressant Treatment Response: Findings from the CO-MED Trial.Molecular neuropsychiatry · 2018Article
- Into the Wild: GWAS Exploration of Non-coding RNAs.Frontiers in cardiovascular medicine · 2018Review
- A functional SNP upstream of theInternational journal of chronic obstructive pulmonary disease · 2018Article
- Article
- A functional variant at the miRNA binding site in HMGB1 gene is associated with risk of oral squamous cell carcinoma.Oncotarget · 2017Article
- Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data.Journal of Alzheimer's disease : JAD · 2017Article
- Functional genetic variant of WW domain-containing oxidoreductase (WWOX) gene is associated with hepatocellular carcinoma risk.PloS one · 2017Article
- SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.PloS one · 2017Article
- Functional genetic variant in the Kozak sequence of WW domain-containing oxidoreductase (WWOX) gene is associated with oral cancer risk.Oncotarget · 2016Article
- Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity.eLife · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
This article illustrates the use of the Encyclopedia of DNA Elements (ENCODE) resource to generate or refine hypotheses from genomic data on disease and other phenotypic traits. First, the goals and history of ENCODE and related epigenomics projects are reviewed. Second, the rationale for ENCODE and the major data types used by ENCODE are briefly described, as are some standard heuristics for their interpretation. Third, the use of the ENCODE resource is examined. Standard use cases for ENCODE, accessing the ENCODE resource, and accessing data from related projects are discussed. Although the focus of this article is the use of ENCODE data, some of the same approaches can be used with data from other projects.
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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.