Annotated Major Model Systems Postranslational Modifications
PTM Proteomics Post Translational Modifications
PTM Protein Post Translational Modifications
Protein Modification Post Translational Modifications
Amino Acids Post Translational Modifications
Keywords
PTM
Protein Modification Database
Posttranslational
Glycosylation Prediction
Phosphoproteome
PTM Proteomics
PTM Protein
Protein Modification
Amino Acids
Protein Post Translational Modifications
This dataset includes protein post-translational modifications as well as associated annotation data obtained from the Biological General Repository for Interaction databases (BIOGRID) for major model organisms species including the type of modification, protein sequence and specific amino acid involved.
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A gene is a localized section of DNA; through a process called transcription, this DNA is copied into a messenger RNA (mRNA). The mRNA is a copy of the gene DNA sequence; mRNA is later translated to a protein through a process called translation. After the translation the protein needs the addition or removal of some elements in order to become active and perform its correct function, these are called post-translational modifications. A protein is conformed by a sequence of amino acids, these modifications are made on specific amino acids on the proteins.
BioGRID interactions are recorded as relationships between two proteins or genes (i.e. they are binary relationships) with an evidence code that supports the interaction and a publication reference. The term “interaction” includes, as well as direct physical binding of two proteins, co-existence in a stable complex and genetic interaction. It should not be assumed that the interaction reported in BioGRID is direct and physical in nature; the experimental system definitions below indicate the nature of the supporting evidence for an interaction between the two biological entities. It should also be noted that some interactions in BioGRID have various levels of evidential support. BioGRID simply curates the result of the experiment from the publication and does not guarantee that any individual interaction is true, well-established or the current consensus view of the community. Curating all available evidence supporting for an interaction enables orthogonal data from various sources to be collated, allowing users of the database to decide confidence in the existence and/or physiological relevance of that interaction.
The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org). BioGRID currently holds over 980,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 55,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. BioGRID provides interaction data from several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases.
Description source: Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O’Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M. The BioGRID interaction database: 2017 update. Nucleic Acids Res. 2016 Dec 14;2017(1) [ Pubmed, NAR ]
About this Dataset
Data Info
Date Created
2015-12-25
Last Modified
2022-02-28
Version
4.4.207
Update Frequency
Quarterly
Temporal Coverage
N/A
Spatial Coverage
N/A
Source
John Snow Labs; Biological General Repository for Interaction Datasets;
Source License URL
Source License Requirements
N/A
Source Citation
N/A
Keywords
PTM, Protein Modification Database, Posttranslational, Glycosylation Prediction, Phosphoproteome, PTM Proteomics, PTM Protein, Protein Modification, Amino Acids
Other Titles
Protein Postranslational Modifications Database, Species Wide Postranslational Modifications, Annotated Major Model Systems Postranslational Modifications, PTM Proteomics Post Translational Modifications, PTM Protein Post Translational Modifications, Protein Modification Post Translational Modifications, Amino Acids Post Translational Modifications
Data Fields
Name
Description
Type
Constraints
Post_Translational_Modification_ID
Biogrid unique identifier for gene postranslational modification.
integer
level : Nominalrequired : 1
Entrez_Gene_ID
Entrez unique identifier for gene the gene which protein has been reported to be postranslational modified. Unique identifier for the gene of the National Center for Biotechnology Information (NCBI)’s Entrez Gene database. This Entrez Gene unique integer can be browsed in the Entrez system online to find nomenclature, sequence, products and other specific details of the gene. The identifier is species specific, a gene ID of a human gene can’t be applied to the same gene of a different species.
integer
level : Nominal
Biogrid_ID
Biogrid database identifier for gene which protein product has been reported to be modified.
integer
level : Nominal
Systematic_Name
Name of the protein given for the experiment.
string
-
Official_Symbol
Short-form abbreviation of the name of the gene coding for the protein. The approved symbols for human genes are collected in the HUGO Gene Nomenclature Committee database; each name and symbol is unique for every gene and can be applied for other species.
string
required : 1
Synonyms
Synonyms for the name of the protein gene involved in postranslational modification
string
-
Sequence
A protein sequence referenced for this PTM Site.
string
-
Ref_Seq_ID
Interactions between genes with reference sequence IDs
string
-
Position
Residue position within the sequence for this PTM Site.
integer
level : Nominal
Post_Translational_Modification
Post-translational modification refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis.
string
-
Residue
The residue that is in location in Position within the Sequence.
string
-
Author
First Author of the publication describing the modification or first author surname of the publication in which the modification has been shown, optionally followed by additional indicators, e.g. Stephenson A (2005).
string
-
Pubmed_ID
Identification number of the text describing the modification published in PubMed database. PubMed is a US National Library of Medicine citation database that contains millions of abstracts, references and full text links of biomedical literature from different trusted sources.
integer
level : Nominal
Organism_ID
Identification number in the BioGrid database for the organism in which the modification was found.
integer
level : Nominal
Organism_Name
Official name for the organism in which the modification was found
string
-
Is_Relationships
PTM Site will have accompanying relationships within the PTMREL data file.
boolean
-
Qualifications
If additional plain text information was recorded for an interaction.
Demos
