ArticlePLoS computational biology2008
In silico detection of sequence variations modifying transcriptional regulation.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 100 citations in OpenAlex.
- GASDERMIN D-mediated pyroptosis as a therapeutic target in TAU-dependent frontotemporal dementia mouse model.Journal of biomedical science · 2026Article
- Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases.Frontiers in bioscience (Scholar edition) · 2024Review
- Identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.iScience · 2023Article
- The Transcription Factor NRF2 Has Epigenetic Regulatory Functions Modulating HDACs, DNMTs, and miRNA Biogenesis.Antioxidants (Basel, Switzerland) · 2023Article
- RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication.Nucleic acids research · 2023Article
- GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.Bioinformatics (Oxford, England) · 2023Article
- Postnatal persistence of nonhuman primate sex-dependent renal structural and molecular changes programmed by intrauterine growth restriction.Journal of medical primatology · 2022Article
- Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression.Genes · 2022Article
- RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis.Nucleic acids research · 2021Article
- A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites.Molecular genetics & genomic medicine · 2020Article
- Predicting the effects of SNPs on transcription factor binding affinity.Bioinformatics (Oxford, England) · 2020Article
- Cannabinoid CBCellular and molecular neurobiology · 2020Article
- CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
- atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding.Bioinformatics (Oxford, England) · 2019Article
- Comprehensive sequencing of the myocilin gene in a selected cohort of severe primary open-angle glaucoma patients.Scientific reports · 2019Article
- CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.BMC bioinformatics · 2019Article
- Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features.Scientific reports · 2018Article
- Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.Cell systems · 2018Article
- Integrating ChIP-seq with other functional genomics data.Briefings in functional genomics · 2018Review
- 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
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 6 institutions in 3 countries.
Funding
Abstract
Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological advances for measuring RNA abundance suggest that a significant number of undiscovered causal mutations may alter the regulation of gene transcription. However, it remains a challenge to separate causal genetic variations from linked neutral variations. Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach combines phylogenetic footprinting and transcription factor binding site prediction to identify variation in candidate cis-regulatory elements. The bioinformatics approach has been tested on a set of SNPs that are reported to have a regulatory function, as well as background SNPs. In the absence of additional information about an analyzed gene, the poor specificity of binding site prediction is prohibitive to its application. However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN (regulatory analysis of variation in enhancers). The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation.
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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.