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Collapse Statistics
226 human active and 11 inactive phosphatases in total;
194 phosphatases have substrate data;
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305 protein substrates;
89 non-protein substrates;
1114 dephosphorylation interactions;
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213 KEGG pathways;
206 NCI Nature PID pathways
560 Reactome pathways;
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last update: 18 Feb, 2016

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About DEPOD

1. Introduction

DEPOD - the human DEPhOsphorylation Database (version 1.1) is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. DEPOD aims to be a valuable resource for studying human phosphatases and their substrate specificities and molecular mechanisms; phosphatase-targeted drug discovery and development; connecting phosphatases with kinases through their common substrates; completing the human phosphorylation/dephosphorylation network.

2. Methodology

A phosphatase is defined as an enzyme that hydrolyzes phosphomonoesters into a phosphate ion and a molecule with a free hydroxyl group. DEPOD focuses on human phosphatases with enzymatic activities, for which the E.C. number is 3.1.3.* (phosphoric monoester hydrolases). These phosphatases not only include protein phosphatases, but also cover phosphatases acting on non-protein substrates like phospholipids and phosphocarbohydrates. These phosphatases are initially retrieved from the Ensembl database. Then the UniProt annotations are manually inspected to identify known active phosphatases.

Known substrates of human phosphatases which have experimental evidences are systematically collected and manually curated from several data sources:

(1) "dephosphorylation" posttranslational modification (PTM) data in Human Protein Reference Database (HPRD);

(2) "dephosphorylation" protein-protein interaction data searched with PSICQUIC (a portal integrating popular protein-protein interaction databases like APID, BioGrid, IntAct, DIP, InnateDB, MPIDB, iRefIndex, MatrixDB, MINT, Interoporc, Reactome, Reactome-FIs, STRING, and BIND);

(3) substrate information from UniProt annotations;

(4) substrate information from literatures searched with PubMed and Google.

For all the potential substrate data, the original literatures are manually checked. Only those supported by in vitro and/or in vivo experimental evidences are kept. A protein substrate was treated as valid only if the whole protein but not the derived peptides were reported to be dephosphorylated.

DEPOD uses a score system for evaluating the reliability of the dephosphorylation interactions. Both the bioassay type (in vitro/in vivo) of dephosphorylation experiments and the number of different laboratories performing the experiments were manually reviewed and considered here. Currently there are three levels: score 1 (star) - in vitro or in vivo experiments performed by single lab, or UniProt annotation; score 2 (starstar): in vitro or in vivo experiments performed by multiple labs or both in vitro and in vivo experiments performed by single lab; score 3 (starstarstar): both in vitro and in vivo experiments performed by multiple labs.

For each protein substrate, DEPOD provides link to the UniProt entry. Both the gene/protein names and the source organisms of substrates are manually inspected in original literatures to locate the correct UniProt entry. For protein substrates, the dephosphorylation sites which are documented in original literatures are also provided in DEPOD. These sites are manually corrected to the corresponding amino acid positions in the sequence of given UniProt protein entry.

For phosphatases in DEPOD, their subcellular localizations are retrieved from UniProt annotations and the LocDB database. Only experimental annotations with original literature information are considered here. For phosphatases, DEPOD also gives links to ChEMBL which is a database listing bioactive molecules and thus provides fast access to research tools of phosphatases.

DEPOD provides links for phosphatases and substrates to three popular kinase databases: Phospho.ELM, PhosphoSite, and NetworKIN. Kinases can be directly retrieved to connect these phosphorylation/dephosphorylation pairs. DEPOD also provides links for phosphatases and substrates to three popular protein-protein interaction databases: STRING, IntAct, and MINT. Their interacting partners can be easily explored to find potential dephosphorylation interactions and study them in a systematic way.

For phosphatases and substrates in DEPOD, the pathways from KEGG Pathway database, NCI Nature Pathway Interaction Database (PID) and Reactome Pathway Database are mapped on them. The mapping results are given in two forms in DEPOD: (1) for each phosphatase or substrate, the pathways in which they are involved are listed; (2) for each pathway, the involved phosphatases and substrates are listed together with their corresponding substrates and phosphatases.

3. Data Sources, External Links and Softwares

Gene Databases
Ensembl Entrez Gene HGNC Gene Ontology QuickGO Gene Expression Atlas The Human Protein Atlas OMIM
Protein Databases
UniProt PIR IntEnz BRENDA LocDB Catalytic Site Atlas InterPro Pfam
Structure Databases
CATH  Gene3D  PDB  PDBe  DrugPort  ModBase SwissModel  
Small Molecule Databases
ChEBI  ChEMBL             
Kinase/Phosphorylation Databases
Phospho.ELM  PhosphoSitePlus  NetwoKIN           
Protein-Protein Interaction Databases
HPRD  PSICQUIC  STRING  IntAct  MINT       
Pathway Databases
NCI Nature PathwayInteractionDatabase  KEGG Pathway  Reactome Pathway Database           
Literature Databases
PubMed  Europe PubMed Central               
Motif Databases
ELM               
Softwares
Cytoscape Web wwwblast OpenAstexViewer jQuery / jQuery UI idTabs FancyBox jquery-powerFloat

4. Funding Sources

DEPOD was started as a part of the collaborative project between three groups: the Thornton Group (EMBL-EBI, Hinxton, UK), the Köhn Group (Faculty of Biology and BIOSS, University of Freiburg) and the Wilmanns Group (EMBL, Hamburg, Germany).

This work was supported by the EMBL and Marie Curie Actions funded EMBL Interdisciplinary Postdoc (EIPOD) fellowship for Dr. Xun Li.

The database is supported by the Excellence Initiave of the German Federal and State Governments (Grant EXC-294 BIOSS Centre for Biological Signalling Studies).

The database is currently maintained and updated by Dr. Guangyou Duan, IMIA net based solutions and Köhn Group (Faculty of Biology and BIOSS, University of Freiburg).

5. Feedback and data deposition

In order to help with the curation of the database, we would like to encourage experts to submit their data about new substrates. For new data entries provided by external experts, we offer to give credit for the contribution on the webpage and in the acknowledgements of further published updates.

6. DEPOD Publications

Duan, G., Li, X., Köhn, M. (2015). The human DEPhOsphorylation database DEPOD: a 2015 update. Nucleic Acids Research, 43(Database issue):D531-5. (PMID: 25332398)

Li X, Wilmanns M, Thornton J, Köhn M. (2013). Elucidating human phosphatase-substrate networks. Science Signaling, 6(275):rs10. (PMID: 23674824)

EMBL-EBI EMBL BIOSS Uni-Freiburg Uni-Freiburg Marie Curie Actions

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