Data sources

• ID Converter (Human, Mouse, Rat)
  • Current release of Uniprot, for idmapping_selected.tab and idmapping.dat for Human, Mouse and Rat: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism
  • All previous release of uniprot can be found here: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/
  • nextprot_ac_list_all.txt (Nextprot released on 13/02/2019 - current): ftp://ftp.nextprot.org/pub/current_release/ac_lists/
  • All previous release of nextprot_ac_list_all.txt can be foud here: ftp://ftp.nextprot.org/pub/previous_releases/
  • Human uniprot-AC entries reviewed (05/06/2019) 
  • Mouse uniprot-AC entries reviewed (05/06/2019) 
  • Rat uniprot-AC entries reviewed (05/06/2019) 
  • Human uniprot-AC entries reviewed (08/05/2019)
  • Mouse uniprot-AC entries reviewed (08/05/2019)
  • Rat uniprot-AC entries reviewed (08/05/2019)
  • Human uniprot-AC entries reviewed (10/10/2018)
  • Mouse uniprot-AC entries reviewed (10/10/2018)
  • Rat uniprot-AC entries reviewed (10/10/2018)

• Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]
  • Normal_tissue: 
    • Human Protein Atlas version 18.1 and Ensembl version 88.38
    • Human Protein Atlas version 19 and Ensembl version 92.38
  • Pathology:
    • Human Protein Atlas version 18.1 and Ensembl version 88.38
    • Human Protein Atlas version 19 and Ensembl version 92.38
  • ProteinAtlas: 
    • Human Protein Atlas version 18.1 and Ensembl version 88.38

• Add expression data (RNAseq or Immuno-assays)[Human Protein Atlas]
  • ProteinAtlas

• Add protein features [neXtProt]
  • nextprot_ac_list.txt : ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt

• Build tissue-specific expression dataset [Human Protein Atlas][neXtProt]
  • The data is based on the Human Protein Atlas version 18 and Ensembl version 88.38. For more information, click here

• Get MS/MS observations in tissue/fluid [Peptide Atlas]
  • Human Adrenal Gland 2014-08
  • Human Brain 2015-01
  • Human Breast 2014-08
  • Human CSF 2014-09
  • Human Colon Cancer 2013-02
  • Human Digestive System 2014-08
  • Human Female Reproductive System 2014-08
  • Human Heart 2014-08
  • Human Kidney 2014-08
  • Human Liver 2014-08
  • Human Lung 2014-08
  • Human Male Reproductive System 2014-08
  • Human Pancreas 2014-08
  • Human Plasma Non-Glyco 2017-04
  • Human Spleen 2014-08
  • Human Testis 2017-01
  • Human Urinary Bladder 2014-08
  • Human Urine 2014-08

• Add protein features (Mouse) [UniProt]
  • Annotations have been retrieved from UniProt.org (02/2019)

• GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]
  • bioconductor-org.hs.eg.db v3.5.0
  • bioconductor-org.mm.eg.db v3.5.0
  • bioconductor-org.rn.eg.db v3.5.0

• Statistical analysis of functional profiles (Human, Mouse) [goProfiles] 
  • bioconductor-org.hs.eg.db v3.5.0
  • bioconductor-org.mm.eg.db v3.5.0

• Enrichment analysis for Gene Ontology (Human, Mouse, Rat)[topGO]
  • bioconductor-org.hs.eg.db v3.5.0
  • bioconductor-org.mm.eg.db v3.5.0
  • bioconductor-org.rn.eg.db v3.5.0

• Query pathway database [Reactome] 
  • Reactome content-service

• Pathways identification and coverage [KEGG]
  • Pathways and KEGG genes IDs are collected via KEGGREST package.

• Pathways visualization of (differentially expressed) genes/proteins [KEGG]
  • KEGG Pathways names list
  • Pathview package doc

• Biogrid
  • BIOGRID-ORGANISM
  • NCBI2Reactome (v67 10-12-18)

• Bioplex
  • BioPlex_interactionList_v4a
  • UniProt2Reactome
  • NCBI2Reactome (v67 10-12-18)

• Humap
  • nodeTable
  • pairsWprob
  • NCBI2Reactome (v67 10-12-18)