ArticleBMC genomics2016
Establishing and validating regulatory regions for variant annotation and expression analysis.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 20 citations in OpenAlex.
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- InCURA: integrative gene clustering based on transcription factor binding sites.Nucleic acids research · 2025Article
- Airborne fine particulate matter exposure induces transcriptomic alterations resembling asthmatic signatures: insights from integrated omics analysis.Environmental epigenetics · 2024Article
- Polycomb protein RYBP activates transcription factorOpen biology · 2023Article
- Article
- Identification of genes, pathways and transcription factor-miRNA-target gene networks and experimental verification in venous thromboembolism.Scientific reports · 2021Article
- Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files.Bioinformatics (Oxford, England) · 2018Article
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.Database : the journal of biological databases and curation · 2017Article
- VarI-SIG 2015: methods for personalized medicine - the role of variant interpretation in research and diagnostics.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe regulatory effect of inherited or de novo genetic variants occurring in promoters as well as in transcribed or even coding gene regions is gaining greater recognition as a contributing factor to disease processes in addition to mutations affecting protein functionality. Thousands of such regulatory mutations are already recorded in HGMD, OMIM, ClinVar and other databases containing published disease causing and associated mutations. It is therefore important to properly annotate genetic variants occurring in experimentally verified and predicted transcription factor binding sites (TFBS) that could thus influence the factor binding event. Selection of the promoter sequence used is an important factor in the analysis as it directly influences the composition of the sequence available for transcription factor binding analysis.
resultsIn this study we first establish genomic regions likely to be involved in regulation of gene expression. TRANSFAC uses a method of virtual transcription start sites (vTSS) calculation to define the best supported promoter for a gene. We have performed a comparison of the virtually calculated promoters between the best supported and secondary promoters in hg19 and hg38 reference genomes to test and validate the approach. Next we create and utilize a workflow for systematic analysis of casual disease associated variants in TFBS using Genome Trax and TRANSFAC databases. A total of 841 and 736 experimentally verified TFBSs within best supported promoters were mapped over HGMD and ClinVar mutation sites respectively. Tens of thousands of predicted ChIP-Seq derived TFBSs were mapped over mutations as well. We have further analyzed some of these mutations for potential gain or loss in transcription factor binding.
conclusionsWe have confirmed the validity of TRANSFAC's approach to define the best supported promoters and established a workflow of their use in annotation of regulatory genetic variants.
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