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Sci Data. 2018 Jul 24;5:180141. doi: 10.1038/sdata.2018.141.

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations.

Author information

1
Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada.
2
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.
3
Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway.

Abstract

Interpreting the functional impact of noncoding variants is an ongoing challenge in the field of genome analysis. With most noncoding variants associated with complex traits and disease residing in regulatory regions, altered transcription factor (TF) binding has been proposed as a mechanism of action. It is therefore imperative to develop methods that predict the impact of noncoding variants at TF binding sites (TFBSs). Here, we describe the update of our MANTA database that stores: 1) TFBS predictions in the human genome, and 2) the potential impact on TF binding for all possible single nucleotide variants (SNVs) at these TFBSs. TFBSs were predicted by combining experimental ChIP-seq data from ReMap and computational position weight matrices (PWMs) derived from JASPAR. Impact of SNVs at these TFBSs was assessed by means of PWM scores computed on the alternate alleles. The updated database, MANTA2, provides the scientific community with a critical map of TFBSs and SNV impact scores to improve the interpretation of noncoding variants in the human genome.

PMID:
30040077
PMCID:
PMC6057437
DOI:
10.1038/sdata.2018.141
[Indexed for MEDLINE]
Free PMC Article

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