ProteoRE tools: public resources release

ID Converter (Human, Mouse, Rat)

• 14/06/2024 - ID mapping files from Uniprot (idmapping_selected.tab, idmapping.dat) Mouse and Rat
• 16/06/2021 - ID mapping files from Uniprot (idmapping_selected.tab, idmapping.dat) Human, Mouse and Rat
• 24/08/2020 - ID mapping files from Uniprot (idmapping_selected.tab, idmapping.dat) Human, Mouse and Rat
• 18/12/2019 - ID mapping files from Uniprot (idmapping_selected.tab, idmapping.dat) Human, Mouse and Rat
• Uniprot_current_release; Uniprot_previous_releases

Add protein features [neXtProt, Human]

• nextProt version:
  • 17/06/2021 (corresponds to neXtProt release 01/03/2021)
  • 31/07/2020 (corresponds to neXtProt release 05/02/2020)
  • 07/05/2019 (corresponds to neXtProt release 13/02/2019)
  • 08/10/2018 (corresponds to neXtProt release 08/10/2018)
• neXtProt_previous_releases

Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]

• Human Protein Atlas version:
• 14/06/2024 based on the Human Protein Atlas version 19.3 and Ensembl version 92.38
• 17/06/2021 based on the Human Protein Atlas version 19.2 and Ensembl version 92.38
• 04/05/2020 based on the Human Protein Atlas version 19.1 and Ensembl version 92.38
• 23/10/2018 based on the Human Protein Atlas version 18.1 and Ensembl version 88.38
• HPA files: Normal_tissue, Pathology and ProteinAtlas files

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

• Human Protein Atlas version:
• 14/06/2024 based on the Human Protein Atlas version 19.3 and Ensembl version 92.38
• 17/06/2021 based on the Human Protein Atlas version 19.2 and Ensembl version 92.38
• 04/05/2020 based on the Human Protein Atlas version 19.1 and Ensembl version 92.38
• 23/10/2018 based on the Human Protein Atlas version 18.1 and Ensembl version 88.38
• More information about Human Protein Atlas here

Build tissue-specific expression dataset [Human Protein Atlas]

• Human Protein Atlas version:
• 14/06/2024 based on the Human Protein Atlas version 19.3 and Ensembl version 92.38
• 17/06/2021 based on the Human Protein Atlas version 19.2 and Ensembl version 92.38
• 04/05/2020 based on the Human Protein Atlas version 19.1 and Ensembl version 92.38
• 23/10/2018 based on the Human Protein Atlas version 18.1 and Ensembl version 88.38
• Human Protein Atlas file name: IHC data: normal_tissue.tsv.zip ; RNAseq data: rna_tissue.tsv.zip

Add protein features (Human, Mouse, Rat) [UniProt]

• Annotations have been retrieved from UniProt (December 2019)

Get MS/MS observations in tissue/fluid [Human 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

Get unique peptide SRM-MRM method [Human SRM Atlas]

• This tool is using the following source file: HumanSRMAtlasPeptidesFinalAnnotated (2016-04) (Kusebauch et al., 2016, PMID: 27453469); http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx

GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]

• bioconductor-org.hs.eg.db v3.8.2
• bioconductor-org.mm.eg.db v3.8.2
• bioconductor-org.rn.eg.db v3.8.2
• dose v3.10.2
• clusterprofiler v 3.12.0

Statistical analysis of functional profiles (Human, Mouse) [goProfiles]

• bioconductor-org.hs.eg.db v3.8.2
• bioconductor-org.mm.eg.db v3.8.2
• bioconductor-annotationdbi v1.40.0
• bioconductor-biobase v2.98.0

Enrichment analysis for Gene Ontology (Human, Mouse, Rat)[topGO]

• bioconductor-org.hs.eg.db v3.8.2
• bioconductor-org.mm.eg.db v3.8.2
• bioconductor-org.rn.eg.db v3.8.2
• bioconductor-annotationdbi v1.46.0
• bioconductor-go.db v3.8.2

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: Human, Mouse, Rattus: downloaded 14/06/2024
• BIOGRID-ORGANISM: Human, Mouse, Rattus: downloaded 17/06/2021
• BIOGRID-ORGANISM: Human, Mouse, Rattus: downloaded 05/02/2020
• BIOGRID-ORGANISM: Human, Mouse, Rattus: downloaded 01/03/2019
• NCBI2Reactome (v67 10-12-18)

Bioplex

• BioPlex_interactionList_v4a.tsv: Version 2.0
• UniProt2Reactome
• NCBI2Reactome (v67 10-12-18)

Humap (Human Protein Complex Map

• nodeTable
• pairsWprob
• downloaded from : http://hu.proteincomplexes.org/download