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SNP2TFBS specifications

Information


Unique identifier OMICS_28871
Name SNP2TFBS
Interface Web user interface
Restrictions to use None
Input data A rsID code, a SNP set or a motif.
Input format VCF, BED
Output data A or some TF(s) with score difference or variability plots or a model.
Output format BED,TSV
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • PWNViewer
  • SNPViewer
  • SNSelect

SNP2TFBS citations

 (13)
library_books

Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice

2018
BMC Genomics
PMCID: 5923191
PMID: 29703142
DOI: 10.1186/s12864-018-4667-0

[…] 17.Ensembl genome browser. http://www.ensembl.org/index.html. Accessed 15 Jun 2017.IMPC | International Mouse Phenotyping Consortium. http://www.mousephenotype.org/. Accessed 15 Jun 2017.Sanger Mouse SnpViewer. http://www.sanger.ac.uk/sanger/Mouse_SnpViewer/rel-1505. Accessed 15 Jun 2017.MGI-Mouse Genome Informatics-The international database resource for the laboratory mouse. http://www.informati […]

library_books

Integrative analysis of super enhancer SNPs for type 2 diabetes

2018
PLoS One
PMCID: 5792005
PMID: 29385209
DOI: 10.1371/journal.pone.0192105

[…] ly predicted regulation features, therefore the model and algorithm selection is critical for this kind of analysis. For example, the reliability of the transcription factor binding site predicted by SNP2TFBS is a function of the accuracy of the PWM model which is less accurate than recently proposed approaches []. Further, genomic sequence with higher affinity to a transcription factor is often i […]

library_books

Single‐nucleotide polymorphism discovery and panel characterization in the African forest elephant

2018
Ecol Evol
PMCID: 5817121
PMID: 29468037
DOI: 10.1002/ece3.3854

[…] or automatic allele calling usually result in a high proportion of unassigned genotype calls (Semagn, Babu, Hearne, & Olsen, ). Therefore, the genotype plots of each assay were visually checked using SNPviewer 2 software (LGC Genomics) and rescored manually if individuals that clearly belonged to a cluster had not been called automatically. The proportions of manually rescored genotypes and missin […]

call_split

COMT genotype and non recovery after a whiplash injury in a Northern European population

2017
PMCID: 5709856
PMID: 29195501
DOI: 10.1186/s12891-017-1810-z
call_split See protocol

[…] petitive allele-specific PCR (KASPar) assay (KBioscience®), based on a public genome sequence (www.ensembl.org/), was used to analyse the SNPs rs6269, rs4633 and rs4818. Alleles were determined using SNPviewer2®. χ2 test or Fisher’s test was used to investigate deviations from Hardy-Weinberg Equilibrium (HWE). The EM algorithm was computed using SNP & Variation Suite 7 (Golden Helix) to estimate l […]

library_books

Genome wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus

2017
Nat Commun
PMCID: 5688097
PMID: 29142228
DOI: 10.1038/s41467-017-01818-4

[…] notations for the Roadmap ChromHMM 15-states and relevant histone marks. We implemented predictions of potentially regulatory effects of QTL-SNPs due to genetic variation of TFBS affinities using the SNP2TFBS database. In total, 857 cis-meQTL-SNPs and 44 cis-eQTL-SNPs with CADD-scores >5 were predicted to alter TFBSs (Supplementary Datas  and ). Consistent with an enrichment of cis-meQTL-CpGs in t […]

library_books

Congenital Cataract in Gpr161vl/vl Mice Is Modified by Proximal Chromosome 15

2017
PLoS One
PMCID: 5279759
PMID: 28135291
DOI: 10.1371/journal.pone.0170724

[…] titute has used next-generation sequencing to sequence key laboratory mouse strains including C3H/HeJ and MOLF/EiJ, and the data were uploaded to a query website (http://www.sanger.ac.uk/sanger/Mouse_SnpViewer/rel-1410). For identification of coding genetic variants, the minimal cataract modifying interval (Chr15: 13062568–28269407) as determined by subcongenic analysis was searched in the query s […]

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