title: SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity.
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/.
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.|Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Sunil
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.|Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Ambrosini
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland philipp.bucher@epfl.ch.|Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism; D064878:Web Browser
chemical_list: D014157:Transcription Factors