Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.

Пономаренко, М. П.; Ponomarenko, Julia; Frolov, Anatoly S.; Podkolodnaya, O. A.; Vorobyev, Denis; Колчанов, Н. А.; Overton, Gail

doi:10.1093/bioinformatics/15.7.631

Cited by 34 publications

(18 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most of them rank unannotated SNPs by their generalized statistical similarity with biomedical SNP markers of human diseases; these Web services evaluate this similarity by superimposing SNPs on gene maps and on data from massively parallel high-throughput sequencing of chromatin immunoprecipitation material (ChIP-Seq) from experiments with complexes of various proteins with genomic DNA. Accuracy of such assessments is constantly increasing due to improvements in empirical formulas for whole-genome evaluation of similarity among pathological manifestations of various SNPs and due to the increasing diversity, completeness, and number of whole-genome maps for various epigenetic states of cells from various tissues and organs in health [150], during infection [151] (or other diseases [152]), or after treatment [153], as we predicted [154] on the basis of the Central Limit Theorem.…”

Section: Resultsmentioning

confidence: 99%

Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

Пономаренко

Рассказов

Суслов

et al. 2016

BioMed Research International

View full text Add to dashboard Cite

Variations in human genome (e.g., single nucleotide polymorphisms, SNPs) may be associated with hereditary diseases, their complications, comorbidities, and drug responses. Using Web service SNP_TATA_Comparator presented in our previous paper, here we analyzed immediate surroundings of known SNP markers of diseases and identified several candidate SNP markers that can significantly change the affinity of TATA-binding protein for human gene promoters, with circadian consequences. For example, rs572527200 may be related to asthma, where symptoms are circadian (worse at night), and rs367732974 may be associated with heart attacks that are characterized by a circadian preference (early morning). By the same method, we analyzed the 90 bp proximal promoter region of each protein-coding transcript of each human gene of the circadian clock core. This analysis yielded 53 candidate SNP markers, such as rs181985043 (susceptibility to acute Q fever in male patients), rs192518038 (higher risk of a heart attack in patients with diabetes), and rs374778785 (emphysema and lung cancer in smokers). If they are properly validated according to clinical standards, these candidate SNP markers may turn out to be useful for physicians (to select optimal treatment for each patient) and for the general population (to choose a lifestyle preventing possible circadian complications of diseases).

show abstract

Section: Resultsmentioning

confidence: 99%

Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

Пономаренко

Рассказов

Суслов

et al. 2016

BioMed Research International

View full text Add to dashboard Cite

show abstract

“…A further theoretical analysis of the nucleotide sequences of the allelic states of the region in question was performed using a method developed for averaging nucleotide and dinucleotide frequencies at the positions of the site in question [24]. The original data were 27 DNA fragments experimentally found to contain the transcription factor YY-1 binding site [30].…”

Section: Resultsmentioning

confidence: 99%

“…A method based on the averaging of oligonucleotide frequencies at each position of the functional sites of DNA was used for recognition of these sites [24]. The initial data for the method to start working are a set of N aligned DNA sequences of length L of the site in question { S n =( s n ; i )} i =1, L ; n =1, N .…”

Section: Methodsmentioning

confidence: 99%

Point mutations within 663–666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY‐1 transcription factor binding site

et al. 1999

View full text Add to dashboard Cite

Single base mutations GC CA at position 663 and GC CT at position 666 of intron 6 of the human tryptophan oxygenase gene (TDO2) are associated with a variety of psychiatric disorders [Comings, D.E. et al. (1996) Pharmacogenetics 6, 307^318]. Binding of rat liver nuclear extract proteins to synthetic double-strand oligonucleotides corresponding to three allelic states of the region between 651 bp and 680 bp of human TDO2 intron 6 has been studied by gel shift assay. It has been demonstrated that to each allelic state of the region there corresponds a specific set of proteins that interacts with it. With the aid of computer analysis and using specific anti-YY-1 antibodies it has been shown that both mutations damage the YY-1 transcription factor binding site.z 1999 Federation of European Biochemical Societies.

show abstract

“…These tools take into account whole-genome maps of genes [13, 14], protein-binding sites, interchromosomal contacts, nucleosomes, and transcripts either in health [40], during infection [41] (or other disease [42]), or after treatment [43]. According to the Central Limit Theorem, the accuracy of this similarity-based search for candidate SNP markers increases with the increase in the number of genome-wide maps [44]. …”

Section: Introductionmentioning

confidence: 99%

Candidate SNP markers of aggressiveness-related complications and comorbidities of genetic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

et al. 2016

View full text Add to dashboard Cite

BackgroundAggressiveness in humans is a hereditary behavioral trait that mobilizes all systems of the body—first of all, the nervous and endocrine systems, and then the respiratory, vascular, muscular, and others—e.g., for the defense of oneself, children, family, shelter, territory, and other possessions as well as personal interests. The level of aggressiveness of a person determines many other characteristics of quality of life and lifespan, acting as a stress factor. Aggressive behavior depends on many parameters such as age, gender, diseases and treatment, diet, and environmental conditions. Among them, genetic factors are believed to be the main parameters that are well-studied at the factual level, but in actuality, genome-wide studies of aggressive behavior appeared relatively recently. One of the biggest projects of the modern science—1000 Genomes—involves identification of single nucleotide polymorphisms (SNPs), i.e., differences of individual genomes from the reference genome. SNPs can be associated with hereditary diseases, their complications, comorbidities, and responses to stress or a drug. Clinical comparisons between cohorts of patients and healthy volunteers (as a control) allow for identifying SNPs whose allele frequencies significantly separate them from one another as markers of the above conditions. Computer-based preliminary analysis of millions of SNPs detected by the 1000 Genomes project can accelerate clinical search for SNP markers due to preliminary whole-genome search for the most meaningful candidate SNP markers and discarding of neutral and poorly substantiated SNPs.ResultsHere, we combine two computer-based search methods for SNPs (that alter gene expression) {i} Web service SNP_TATA_Comparator (DNA sequence analysis) and {ii} PubMed-based manual search for articles on aggressiveness using heuristic keywords. Near the known binding sites for TATA-binding protein (TBP) in human gene promoters, we found aggressiveness-related candidate SNP markers, including rs1143627 (associated with higher aggressiveness in patients undergoing cytokine immunotherapy), rs544850971 (higher aggressiveness in old women taking lipid-lowering medication), and rs10895068 (childhood aggressiveness-related obesity in adolescence with cardiovascular complications in adulthood).ConclusionsAfter validation of these candidate markers by clinical protocols, these SNPs may become useful for physicians (may help to improve treatment of patients) and for the general population (a lifestyle choice preventing aggressiveness-related complications).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3353-3) contains supplementary material, which is available to authorized users.

show abstract

Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.

Abstract: The MATRIX database is available on the Web, http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.

Cited by 34 publications

References 0 publications

Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

Point mutations within 663–666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY‐1 transcription factor binding site

Candidate SNP markers of aggressiveness-related complications and comorbidities of genetic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

Contact Info

Product

Resources

About