Journal article Open Access

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

Laurens Wiel; Coos Baakman; Daan Gilissen; Joris A. Veltman; Gerrit Vriend; Christian Gilissen

Data manager(s)
Laurens Wiel

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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