Published May 22, 2019 | Version v1.0.1_hg19
Journal article Open

MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains

Creators

  • 1. Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
  • 2. Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
  • 3. Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Bio-informatica, HAN University of Applied Sciences, Nijmegen, The Netherlands
  • 4. Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
  • 5. Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands

Contributors

Data manager:

  • 1. Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA

Description

Entire .tsv data representation for the MetaDome web server v1.0.1 based on GENCODE Release 19 (GRCh37.p13), gnomAD r2.0.2, and Pfam 30.0

Columns:

  • chrom : Chromosome in 'chrN' format with N a number or 'X'/'Y'
  • pos_start : Genomic starting position of a codon in 'gencode_transcription_id'
  • pos_stop : Genomic stop position of a codon in 'gencode_transcription_id'
  • strand : Strand of the reading frame
  • symbol : HGNC Gene symbol
  • gencode_transcription_id : The gencode transcript that this row corresponds to
  • sw_dn_ds : Dn/Ds score based on gnomAD missense and synonymous variants computed over a sliding windows with coverage 'sw_coverage' and size 'sw_size' left and right of this particular codon
  • sw_coverage : Coverage of the sliding size 'sw_size' (This is < 1.0 at start or end of coding region)
  • sw_size : Sliding window size in number of amino acids or codons left and right of the current annotation
  • domain_id : A Pfam domain identifier if this codon is part of a Pfam protein domain, otherwise '' 
  • consensus_pos : A Pfam domain consensus position in perspective of the 'domain_id' identifier. The consensus position indicates a evolutionary equivalent position.

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Preprint: 10.1101/509935 (DOI)