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Datasets

Compilations

Time series

  • Physionet
  • 2019 BEAT PD Dream Challenge (predict Parkonson's disease from sensor data).
  • XTX Challenge (predict stock market tick data)

Genome Variation

Broad Firehose

  • Download data using {firehose client}.

Cosmic

  • Includes data from TCGA, ICGC and manual curation.

ExAC

GDC

  • TCGA and other data.
  • Download data using gdc-client

ICGC

  • Download data from portal.

T-cell receptor repertoires

  • VDJdb - VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. [paper]

Protein-protein interaction

  • BioGrid — Protein-protein interaction data collected from multiple sources.
  • Mentha — Mentha is a database of protein-protein interactions. Mentha combines data from several databases in the IMEx consortium and converts gene names to UniProt identifiers.
  • STRING — Protein-protein interaction network, with every interaction assigned a probability score based on difference evidence channels.
  • HuRI — The Human Reference Protein Interactome Mapping Project. Genome-wide screening of pairwise interactions using yeast two-hybrid.

Protein-small molecule interaction

  • STITCH — Protein-small molecule interaction data integrated from multiple sources and assigned a probability score.

Gene-disease associations

  • DISEASES - Disease-gene associations mined from the literature.
  • DisGeNet - Uses USMLE identifiers with mapping to DO and HPO.
  • DECIPHER - Development Disorder Genotype – Phenotype Database (DDG2P) – a curated list of genes reported to be associated with developmental disorders, compiled by clinicians as part of the DDD study to facilitate clinical feedback of likely causal variants.
  • PhenomeCentral
  • Matchmaker Exchange
  • Genomic discovery through the exchange of phenotypic and genotypic profiles - The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery ( http://onlinelibrary.wiley.com/doi/10.1002/humu.22858/full)

Ontologies

  • Uberon - An integrated cross-species ontology covering anatomical structures in animals.
  • HPO

Wikipedia

Exploring human genes: