ArticlePloS one2013
Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 49 citations in OpenAlex.
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- Protein network and pathway analysis in a pharmacogenetic study of cyclosporine treatment response in Greek patients with psoriasis.The pharmacogenomics journal · 2023Article
- A Panel of rSNPs Demonstrating Allelic Asymmetry in Both ChIP-seq and RNA-seq Data and the Search for Their Phenotypic Outcomes through Analysis of DEGs.International journal of molecular sciences · 2021Article
- Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases.International journal of molecular sciences · 2021Review
- Genetic variants associated with alcohol dependence co-ordinate regulation of ADH genes in gastrointestinal and adipose tissues.Scientific reports · 2020Article
- CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
- Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.BMC bioinformatics · 2019Article
- Regulatory SNPs and their widespread effects on the transcriptome.Journal of biosciences · 2018Review
- Novel functional variants at the GWAS-implicated loci might confer risk to major depressive disorder, bipolar affective disorder and schizophrenia.BMC neuroscience · 2018Article
- Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters.BMC genomics · 2018Article
- Article
- Regulatory single nucleotide polymorphisms (rSNPs) at the promoters 1A and 1B of the human APC gene.BMC genetics · 2016Article
- Non-coding single nucleotide variants affecting estrogen receptor binding and activity.Genome medicine · 2016Article
- A systematic, large-scale comparison of transcription factor binding site models.BMC genomics · 2016Article
- Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.Frontiers in immunology · 2016Article
- Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.BioMed research international · 2016Article
- ePIANNO: ePIgenomics ANNOtation tool.PloS one · 2016Article
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Authors and funding
7 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
A vast amount of SNPs derived from genome-wide association studies are represented by non-coding ones, therefore exacerbating the need for effective identification of regulatory SNPs (rSNPs) among them. However, this task remains challenging since the regulatory part of the human genome is annotated much poorly as opposed to coding regions. Here we describe an approach aggregating the whole set of ENCODE ChIP-seq data in order to search for rSNPs, and provide the experimental evidence of its efficiency. Its algorithm is based on the assumption that the enrichment of a genomic region with transcription factor binding loci (ChIP-seq peaks) indicates its regulatory function, and thereby SNPs located in this region are more likely to influence transcription regulation. To ensure that the approach preferably selects functionally meaningful SNPs, we performed enrichment analysis of several human SNP datasets associated with phenotypic manifestations. It was shown that all samples are significantly enriched with SNPs falling into the regions of multiple ChIP-seq peaks as compared with the randomly selected SNPs. For experimental verification, 40 SNPs falling into overlapping regions of at least 7 TF binding loci were selected from OMIM. The effect of SNPs on the binding of the DNA fragments containing them to the nuclear proteins from four human cell lines (HepG2, HeLaS3, HCT-116, and K562) has been tested by EMSA. A radical change in the binding pattern has been observed for 29 SNPs, besides, 6 more SNPs also demonstrated less pronounced changes. Taken together, the results demonstrate the effective way to search for potential rSNPs with the aid of ChIP-seq data provided by ENCODE project.
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