Changelog

March 2020 update

Released 15 March 2020

PTM sites

  • Glycosylation sites (N-, O-, S-, C-) were added based on the UniProt (May 2019)
  • Other types of PTM sites were updated using the UniProt data
  • The origin database is now stored and displayed for each PTM site to help users in further investigation, including scrutinizing the evidence quality and citing the original reporters. It can be accessed by hovering over the site in the sequence view:
    ptm_site_source
  • The code for mapping sites across isoforms has been improved and included in the released source code

Mutations

Inherited mutations with clinical significance (from ClinVar)

  • Clinical mutations from ClinVar were updated using May 2019 release (20190520)

  • ClinVar mutations are now stringently filtered to only include clinically relevant, non-somatic mutations. Specifically:

    • mutations with germline, parental, maternal, biparental, etc origin are included; de novo mutations are also included,
    • mutations with a somatic origin, or missing the origin information are excluded (see here for the blacklist),
    • only mutations associated with a disease, or conferring sensitivity (but not resistance) are included (details here)
  • ClinVar mutations include more metadata:

Genes

Gene information (including identifiers mapping to external databases) were updated using the UCSC Genome Browser distributed tables of RefSeq database and the UniProt database.

Sequence view

  • conservation track showing phyloP scores (based on the 100way track from UCSC Genome Browser) was added. The per-aminoacid scores were calculated as an average of the codon scores.

Active genes

  • ActiveDriver results for ClinVar are now computed on the pathogenic/likely pathogenic/drug response subset of mutations

Pathways

  • Reactome and Gene Ontology pathways were updated (8th March 2020)
  • Top pathways were calculated using ActivePathways

Technical aspects

  • BerkeleyDB was replaced with LightningDB offering higher performance for bulk mutations queries
  • The filtering system was updated; If yous saved old URLs including filters, you can still use it with v2017, but new URLs require adjustments.

Data updates tables

  v2017 v2020
Proteins 39 159 39 159
Kinases and other PTM enzymes 678 655
Kinase families 148 143
Mutations    
  3 587 270 3 707 271
ClinVar 137 860 318 428
TCGA MC3 1 595 400 1 595 400
ESP6500 1 318 972 1 318 972
1000 Genomes 1 066 906 1 066 906
Mutations in PTM sites 506 978 826 828
Mutations network-rewiring effect
(losses and gains of sequence motifs)
69 820 70 734
Total number of annotated nucleotides 97 169 994 96 138 347
Pathways 16 662 18 511
Kinase - site interactions 32 925 33 840
Kinases interacting with >= 1 site 441 497
PTM sites 385 185 544 720

 

Data source Update date Use in ActiveDriverDB
InterPro 2019-05-05 Protein domains annotation track
NCBI Gene 2019-05-05 Full gene name/description
DrugBank 2019-05-05 Drug-protein interactions
RefSeq (via UCSC) 2019-05-05 Gene and protein data
phyloP100way (UCSC) 2019-05-05 Conservation track
ClinVar mutations 2019-05-25 Inherited disease mutations
UniProt 2019-05-05 PTM sites, identifiers mapping
ELM 2015-04 Phosphorylation sites
PhosphoSitePlus < 2020 PTM sites
HPRD 2010-07 PTM sites
PTMvar < 2018 PTM sites