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Database Commons - SNP2TFBS

SNP2TFBS

Citations: 0

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Short name SNP2TFBS
Full name
Description a Web interface aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome
URL http://ccg.vital-it.ch/snp2tfbs/
Year founded 2016
Last update & version 2017-01-01    
Availability
University/Institution hosted Switzerland Swiss Institute of Bioinformatics
Address CH-1015
City Lausanne
Province/State Vaud
Country/Region Switzerland
Contact name Philipp Bucher
Contact email philipp.bucher@epfl.ch
Data type(s)
Major organism(s)
Keyword(s)
  • SNP
  • transcription factor binding site
Publication(s)
  • SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity. [PMID: 27899579]

    Sunil Kumar, Giovanna Ambrosini, Philipp Bucher
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-13)

    Abstract: SNP2TFBS is a computational resource intended to support researchers investigating the molecular mechanisms underlying regulatory variation in the human genome. The database essentially consists of a collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. A SNP's effect on TF binding is estimated based on a position weight matrix (PWM) model for the binding specificity of the corresponding factor. These data files are regenerated at regular intervals by an automatic procedure that takes as input a reference genome, a comprehensive SNP catalogue and a collection of PWMs. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. Homepage: http://ccg.vital-it.ch/snp2tfbs/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
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200 OK2017-08-15
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200 OK2017-08-08
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200 OK2017-06-20
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200 OK2017-05-09
200 OK2017-05-05
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200 OK2017-04-28
200 OK2017-04-25
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200 OK2017-04-18
200 OK2017-04-14
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200 OK2017-04-04
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200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14

Tags

Interaction and Network Phenotype
Homo sapiens
SNP transcription factor binding site

Record metadata

  • Created on: 2017-02-13
  • Curated by:
    • Lina Ma [2017-08-02]
    • Shixiang Sun [2017-02-13]
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