Protein Post Translational Modifications

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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 aminoacid involved.

Complexity

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 aminoacides, these modifications are made on specific aminoacids 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 ]

Date Created

2015-12-25

Last Modified

2019-10-30

Version

3.5.178

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

Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID a general repository for interaction datasets. Nucleic Acids Res. 2006 Jan 1;34(Database issue)D535-9. PubMed PMID 16381927. Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M. The BioGRID interaction database 2015 update. Nucleic Acids Res. 2015 Jan;43(Database issue)D470-8. PubMed PMID 25428363

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

NameDescriptionTypeConstraints
Post_Translational_Modification_IDBiogrid unique identifier for gene postranslational modification.integerlevel : Nominal required : 1
Entrez_Gene_IDEntrez 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.integerlevel : Nominal
Biogrid_IDBiogrid database identifier for gene which protein product has been reported to be modified.integerlevel : Nominal
Systematic_NameName of the protein given for the experiment.string-
Official_SymbolShort-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.stringrequired : 1
SynonymsSynonyms for the name of the protein gene involved in postranslational modificationstring-
SequenceA protein sequence referenced for this PTM Site.string-
Ref_Seq_IDInteractions between genes with reference sequence IDsstring-
PositionResidue position within the sequence for this PTM Site.integerlevel : Nominal
Post_Translational_ModificationPost-translational modification refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis.string-
ResidueThe residue that is in location in Position within the Sequence.string-
AuthorFirst 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_IDIdentification 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.integerlevel : Nominal
Organism_IDIdentification number in the BioGrid database for the organism in which the modification was found.integerlevel : Nominal
Organism_NameOfficial name for the organism in which the modification was foundstring-
Is_RelationshipsPTM Site will have accompanying relationships within the PTMREL data file.boolean-
QualificationsIf additional plain text information was recorded for an interaction.string-
Source_DatabaseDatabase from which the data were extracted.string-
Post Translational Modification IDEntrez Gene IDBiogrid IDSystematic NameOfficial SymbolSynonymsSequenceRef Seq IDPositionPost Translational ModificationResidueAuthorPubmed IDOrganism IDOrganism NameIs RelationshipsQualificationsSource Database
185048831091YFL056CAAD6YFL057C|L000004638MADLFAPAPEPSTELGRLRVLSKSAGIRVSPLILGGMSIGDAWSEILGSMSKERAFELLDAFYEAGGNFIDTANNYQNEQSEAWIGEWMVSRKLRDQIVIATKFTTDYKKYDVGGGKSANYCGNHKRSLHVSVRDSLRKLQTDWIDILYVHWWDYMSSIEEVMDSLHILVQQARSSIWVCLIRLPGLFLRQITTLNLMVKPLLASIKVNGTCNP_116599111PhosphorylationYBodenmiller B (2010)21177495559292Saccharomyces cerevisiae (S288c)FalseDeletion of protein Kinase YPL031C/PHO85 causes Fold Change logFC 2.565 - PMID 21177495.PhosphoGRID
285048831091YFL056CAAD6YFL057C|L000004638MADLFAPAPEPSTELGRLRVLSKSAGIRVSPLILGGMSIGDAWSEILGSMSKERAFELLDAFYEAGGNFIDTANNYQNEQSEAWIGEWMVSRKLRDQIVIATKFTTDYKKYDVGGGKSANYCGNHKRSLHVSVRDSLRKLQTDWIDILYVHWWDYMSSIEEVMDSLHILVQQARSSIWVCLIRLPGLFLRQITTLNLMVKPLLASIKVNGTCNP_116599118PhosphorylationSBodenmiller B (2010)21177495559292Saccharomyces cerevisiae (S288c)FalseDeletion of protein Kinase YPL031C/PHO85 causes Fold Change logFC 2.565 - PMID 21177495.PhosphoGRID
385644336479YHR047CAAP1AAP1|L000000006MSREVLPNNVTPLHYDITLEPNFRAFTFEGSLKIDLQINDHSINSVQINYLEIDFHSARIEGVNAIEVNKNENQQKATLVFPNGTFENLGPSAKLEIIFSGILNDQMAGFYRAKYTDKVTGETKYMATTQMEATDARRAFPCFDEPNLKATFAVTLVSESFLTHLSNMDVRNETIKEGKKYTTFNTTPKMSTYLVAFIVADLRYVESNNFRIPVRVYSTPGDEKFGQFAANLAARTLRFFEDTFNIEYPLPKMDMVAVHEFSAGAMENWGLVTYRVIDLLLDIENSSLDRIQRVAEVIQHELAHQWFGNLVTMDWWEGLWLNEGFATWMSWYSCNKFQPEWKVWEQYVTDNLQRALNLDSLRSSHPIEVPVNNADEINQIFDAISYSKGSSLLRMISKWLGEETFIKGVSQYLNKFKYGNAKTGDLWDALADASGKDVCSVMNIWTKRVGFPVLSVKEHKNKITLTQHRYLSTGDVKEEEDTTIYPILLALKDSTGIDNTLVLNEKSATFELKNEEFFKINGDQSGIFITSYSDERWAKLSKQANLLSVEDRVGLVADAKALSASGYTSTTNFLNLISNWKNEDSFVVWEQIINSLSALKSTWVFEPEDILNALDKFTLDLVLNKLSELGWNIGEDDSFAIQRLKVTLFSAACTSGNEKMQSIAVEMFEEYANGNKQAIPALFKAVVFNTVARLGGENNYEKIFNIYQNPVSSEEKIIALRALGRFEDKELLERTLSYLLDGTVLNQDFYIPMQGIRVHKKGIERLWAWMQEHWDEIAKRLQPGSPVLGGVLTLGLTNFTSFEALEKISAFYSRKVTKGFDQTLAQALDTIRSKAQWVSRDREIVATYLREHEYDQNP_011913248PhosphorylationYAlbuquerque CP (2008)18407956559292Saccharomyces cerevisiae (S288c)FalsePhosphoGRID
485375534028YKL106WAAT1aspartate transaminase AAT1|L000000009MLRTRLTNCSLWRPYYTSSLSRVPRAPPDKVLGLSEHFKKVKNVNKIDLTVGIYKDGWGKVTTFPSVAKAQKLIESHLELNKNLSYLPITGSKEFQENVMKFLFKESCPQFGPFYLAHDRISFVQTLSGTGALAVAAKFLALFISRDIWIPDPSWANHKNIFQNNGFENIYRYSYYKDGQIDIDGWIEQLKTFAYNNQQENNKNPPCIILHACCHNPTGLDPTKEQWEKIIDTIYELKMVPIVDMAYQGLESGNLLKDAYLLRLCLNVNKYPNWSNGIFLCQSFAKNMGLYGERVGSLSVITPATANNGKFNPLQQKNSLQQNIDSQLKKIVRGMYSSPPGYGSRVVNVVLSDFKLKQQWFKDVDFMVQRLHHVRQEMFDRLGWPDLVNFAQQHGMFYYTRFSPKQVEILRNNYFVYLTGDGRLSLSGVNDSNVDYLCESLEAVSKMDKLANP_01281662PhosphorylationTHelbig AO (2010)21126336559292Saccharomyces cerevisiae (S288c)FalsePMID 21126336: Predicted protein kinase = RIM11PhosphoGRID
585071431301YLR027CAAT2ASP5|aspartate transaminase AAT2|L000000131|L000002677MSATLFNNIELLPPDALFGIKQRYGQDQRATKVDLGIGAYRDDNGKPWVLPSVKAAEKLIHNDSSYNHEYLGITGLPSLTSNAAKIIFGTQSDAFQEDRVISVQSLSGTGALHISAKFFSKFFPDKLVYLSKPTWANHMAIFENQGLKTATYPYWANETKSLDLNGFLNAIQKAPEGSIFVLHSCAHNPTGLDPTSEQWVQIVDAIASKNHIALFDTAYQGFATGDLDKDAYAVRLGVEKLSTVSPVFVCQSFAKNAGMYGERVGCFHLALTKQAQNKTIKPAVTSQLAKIIRSEVSNPPAYGAKIVAKLLETPELTEQWHKDMVTMSSRITKMRHALRDHLVKLGTPGNWDHIVNQCGMFSFTGLTPQMVKRLEETHAVYLVASGRASIAGLNQGNVEYVAKAIDEVVRFYTIEAKLNP_013127389PhosphorylationSChi A (2007)17287358559292Saccharomyces cerevisiae (S288c)FalsePhosphoGRID
685253832931YBR236CABD1L000000011MSTKPEKPIWMSQEDYDRQYGSITGDESSTVSKKDSKVTANAPGDGNGSLPVLQSSSILTSKVSDLPIEAESGFKIQKRRHERYDQEERLRKQRAQKLREEQLKRHEIEMTANRSINVDQIVREHYNERTIIANRAKRNLSPIIKLRNFNNAIKYMLIDKYTKPGDVVLELGCGKGGDLRKYGAAGISQFIGIDISNASIQEAHKRYRSMRNLDYQVVLITGDCFGESLGVAVEPFPDCRFPCDIVSTQFCLHYAFETEEKARRALLNVAKSLKIGGHFFGTIPDSEFIRYKLNKFPKEVEKPSWGNSIYKVTFENNSYQKNDYEFTSPYGQMYTYWLEDAIDNVPEYVVPFETLRSLADEYGLELVSQMPFNKFFVQEIPKWIERFSPKMREGLQRSDGRYGVEGDEKEAASYFYTMFAFRKVKQYIEPESVKPNNP_00979512PhosphorylationSChen SH (2010)20190278559292Saccharomyces cerevisiae (S288c)TruePhosphoGRID
785374834022YKL112WABF1BAF1|OBF1|REB2|SBF1|DNA-binding protein ABF1|L000000159MDKLVVNYYEYKHPIINKDLAIGAHGGKKFPTLGAWYDVINEYEFQTRCPIILKNSHRNKHFTFACHLKNCPFKVLLSYAGNAASSETSSPSANNNTNPPGTPDHIHHHSNNMNNEDNDNNNGSNNKVSNDSKLDFVTDDLEYHLANTHPDDTNDKVESRSNEVNGNNDDDADANNIFKQQGVTIKNDTEDDSINKASIDRGLDDESGPTHGNDSGNHRHNEEDDVHTQMTKNYSDVVNDEDINVAIANAVANVDSQSNNKHDGKDDDATNNNDGQDNNTNNDHNNNSNINNNNVGSHGISSHSPSSIRDTSMNLDVFNSATDDIPGPFVVTKIEPYHSHPLEDNLSLGKFILTKIPKILQNDLKFDQILESSYNNSNHTVSKFKVSHYVEESGLLDILMQRYGLTAEDFEKRLLSQIARRITTYKARFVLKKKKMGEYNDLQPSSSSNNNNNNDGELSGTNLRSNSIDYAKHQEISSAGTSSNTTKNVNNNKNDSNDDNNGNNNNDASNLMESVLDKTSSHRYQPKKMPSVNKWSKPDQITHSDVSMVGLDESNDGGNENVHPTLAEVDAQEARETAQLAIDKINSYKRSIDDKNGDGHNNSSRNVVDENLINDMDSEDAHKSKRQHLSDITLEERNEDDKLPHEVAEQLRLLSSHLKEVENLHQNNDDDVDDVMVDVDVESQYNKNTTHHNNHHSQPHHDEEDVAGLIGKADDEEDLSDENIQPELRGQNP_012810189PhosphorylationTGnad F (2009)19795423559292Saccharomyces cerevisiae (S288c)FalsePMID 19823750: 5,20 min 0.4M NaCl ratio (log2); 0.699,1.475|PMID 19823750: best predicted motif = FHA1 Rad53p|Deletion of protein Kinase YPL026C/SKS1 causes Fold Change logFC -1.607 - PMID 21177495.PhosphoGRID
885374834022YKL112WABF1BAF1|OBF1|REB2|SBF1|DNA-binding protein ABF1|L000000159MDKLVVNYYEYKHPIINKDLAIGAHGGKKFPTLGAWYDVINEYEFQTRCPIILKNSHRNKHFTFACHLKNCPFKVLLSYAGNAASSETSSPSANNNTNPPGTPDHIHHHSNNMNNEDNDNNNGSNNKVSNDSKLDFVTDDLEYHLANTHPDDTNDKVESRSNEVNGNNDDDADANNIFKQQGVTIKNDTEDDSINKASIDRGLDDESGPTHGNDSGNHRHNEEDDVHTQMTKNYSDVVNDEDINVAIANAVANVDSQSNNKHDGKDDDATNNNDGQDNNTNNDHNNNSNINNNNVGSHGISSHSPSSIRDTSMNLDVFNSATDDIPGPFVVTKIEPYHSHPLEDNLSLGKFILTKIPKILQNDLKFDQILESSYNNSNHTVSKFKVSHYVEESGLLDILMQRYGLTAEDFEKRLLSQIARRITTYKARFVLKKKKMGEYNDLQPSSSSNNNNNNDGELSGTNLRSNSIDYAKHQEISSAGTSSNTTKNVNNNKNDSNDDNNGNNNNDASNLMESVLDKTSSHRYQPKKMPSVNKWSKPDQITHSDVSMVGLDESNDGGNENVHPTLAEVDAQEARETAQLAIDKINSYKRSIDDKNGDGHNNSSRNVVDENLINDMDSEDAHKSKRQHLSDITLEERNEDDKLPHEVAEQLRLLSSHLKEVENLHQNNDDDVDDVMVDVDVESQYNKNTTHHNNHHSQPHHDEEDVAGLIGKADDEEDLSDENIQPELRGQNP_012810189PhosphorylationTBodenmiller B (2010)21177495559292Saccharomyces cerevisiae (S288c)FalsePMID 19823750: 5,20 min 0.4M NaCl ratio (log2); 0.699,1.475|PMID 19823750: best predicted motif = FHA1 Rad53p|Deletion of protein Kinase YPL026C/SKS1 causes Fold Change logFC -1.607 - PMID 21177495.PhosphoGRID
985374834022YKL112WABF1BAF1|OBF1|REB2|SBF1|DNA-binding protein ABF1|L000000159MDKLVVNYYEYKHPIINKDLAIGAHGGKKFPTLGAWYDVINEYEFQTRCPIILKNSHRNKHFTFACHLKNCPFKVLLSYAGNAASSETSSPSANNNTNPPGTPDHIHHHSNNMNNEDNDNNNGSNNKVSNDSKLDFVTDDLEYHLANTHPDDTNDKVESRSNEVNGNNDDDADANNIFKQQGVTIKNDTEDDSINKASIDRGLDDESGPTHGNDSGNHRHNEEDDVHTQMTKNYSDVVNDEDINVAIANAVANVDSQSNNKHDGKDDDATNNNDGQDNNTNNDHNNNSNINNNNVGSHGISSHSPSSIRDTSMNLDVFNSATDDIPGPFVVTKIEPYHSHPLEDNLSLGKFILTKIPKILQNDLKFDQILESSYNNSNHTVSKFKVSHYVEESGLLDILMQRYGLTAEDFEKRLLSQIARRITTYKARFVLKKKKMGEYNDLQPSSSSNNNNNNDGELSGTNLRSNSIDYAKHQEISSAGTSSNTTKNVNNNKNDSNDDNNGNNNNDASNLMESVLDKTSSHRYQPKKMPSVNKWSKPDQITHSDVSMVGLDESNDGGNENVHPTLAEVDAQEARETAQLAIDKINSYKRSIDDKNGDGHNNSSRNVVDENLINDMDSEDAHKSKRQHLSDITLEERNEDDKLPHEVAEQLRLLSSHLKEVENLHQNNDDDVDDVMVDVDVESQYNKNTTHHNNHHSQPHHDEEDVAGLIGKADDEEDLSDENIQPELRGQNP_012810189PhosphorylationTSoufi B (2009)19823750559292Saccharomyces cerevisiae (S288c)FalsePMID 19823750: 5,20 min 0.4M NaCl ratio (log2); 0.699,1.475|PMID 19823750: best predicted motif = FHA1 Rad53p|Deletion of protein Kinase YPL026C/SKS1 causes Fold Change logFC -1.607 - PMID 21177495.PhosphoGRID
1085374834022YKL112WABF1BAF1|OBF1|REB2|SBF1|DNA-binding protein ABF1|L000000159MDKLVVNYYEYKHPIINKDLAIGAHGGKKFPTLGAWYDVINEYEFQTRCPIILKNSHRNKHFTFACHLKNCPFKVLLSYAGNAASSETSSPSANNNTNPPGTPDHIHHHSNNMNNEDNDNNNGSNNKVSNDSKLDFVTDDLEYHLANTHPDDTNDKVESRSNEVNGNNDDDADANNIFKQQGVTIKNDTEDDSINKASIDRGLDDESGPTHGNDSGNHRHNEEDDVHTQMTKNYSDVVNDEDINVAIANAVANVDSQSNNKHDGKDDDATNNNDGQDNNTNNDHNNNSNINNNNVGSHGISSHSPSSIRDTSMNLDVFNSATDDIPGPFVVTKIEPYHSHPLEDNLSLGKFILTKIPKILQNDLKFDQILESSYNNSNHTVSKFKVSHYVEESGLLDILMQRYGLTAEDFEKRLLSQIARRITTYKARFVLKKKKMGEYNDLQPSSSSNNNNNNDGELSGTNLRSNSIDYAKHQEISSAGTSSNTTKNVNNNKNDSNDDNNGNNNNDASNLMESVLDKTSSHRYQPKKMPSVNKWSKPDQITHSDVSMVGLDESNDGGNENVHPTLAEVDAQEARETAQLAIDKINSYKRSIDDKNGDGHNNSSRNVVDENLINDMDSEDAHKSKRQHLSDITLEERNEDDKLPHEVAEQLRLLSSHLKEVENLHQNNDDDVDDVMVDVDVESQYNKNTTHHNNHHSQPHHDEEDVAGLIGKADDEEDLSDENIQPELRGQNP_012810189PhosphorylationTAlbuquerque CP (2008)18407956559292Saccharomyces cerevisiae (S288c)FalsePMID 19823750: 5,20 min 0.4M NaCl ratio (log2); 0.699,1.475|PMID 19823750: best predicted motif = FHA1 Rad53p|Deletion of protein Kinase YPL026C/SKS1 causes Fold Change logFC -1.607 - PMID 21177495.PhosphoGRID