SNP2TFBS protocols

View SNP2TFBS computational protocol

SNP2TFBS statistics

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Associated diseases

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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 in pipeline

2017
PMCID: 5886296
PMID: 29228333
DOI: 10.1093/hmg/ddx422

[…] analysed in tem where available., affymetrix 6.0 snp microarray analysis v.6.0 (affymetrix) was performed for both affected individuals in family a. data analysis was carried out using snpviewer v0.9.2 (https://sourceforge.net/projects/snpviewer/) to identify shared regions of homozygosity. this created a visual output plus numerical chromosome coordinates of regions of interest., […]


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SNP2TFBS in publications

 (38)
PMCID: 5923191
PMID: 29703142
DOI: 10.1186/s12864-018-4667-0

[…] 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. […]

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

[…] snps on gene expression (eqtls) and regulatory motif alterations within sets of genetically linked t2d super enhancer snps. furthermore, we performed transcription factor enrichment analysis using snp2tfbs (http://ccg.vital-it.ch/snp2tfbs/) tool which selects and visualizes user defined variants that affect single or multiple transcription factors., gwas3d (http://jjwanglab.org/gwas3d) […]

PMCID: 5817121
PMID: 29468037
DOI: 10.1002/ece3.3854

[…] 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 […]

PMCID: 5919737
PMID: 29242385
DOI: 10.1534/g3.117.300507

[…] cq values, and fold change in expression of a/j and 129s1/svimj over c57bl/6j was calculated., we utilized the sanger mouse genomes project variant database () (http://www.sanger.ac.uk/sanger/mouse_snpviewer/rel-1505) to identify variants within our cloned promoter region, which spans 29783622–29784093 bp on chromosome 7. these variants are shown in ., the sanger mouse genomes project variant […]

PMCID: 5709856
PMID: 29195501
DOI: 10.1186/s12891-017-1810-z

[…] 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) […]


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