The statistics of PTM sites in dbPTM

The dbPTM has been maintained for over ten years with an attempt to provide comprehensively functional and structural analyses for post-translational modifications (PTMs). In this update, dbPTM not only integrate more experimentally validated PTMs from available databases and manual curation of literature, but also provide disease association based on non-synonymous single nucleotide polymorphisms (nsSNPs). The high-throughput deep sequencing technology has leaded the analysis of association between SNPs and diseases into a data surge in both growth and scope. This update thus integrated disease-associated nsSNPs from dbSNP based on Genome-Wide Association Studies (GWAS). The PTM substrate sites locating in a specified distance of the amino acids encoded from nsSNPs were referred to having an association with its involving diseases.



The statistics of experimental and putative PTM sites in dbPTM

PTM TypeNumber of experimental sitesNumber of putative sitesTotal sites of the typeNumber of literatures
Phosphorylation571,032121,330692,36252,381
Acetylation137,44228,811166,25321,251
Ubiquitination118,49534,950153,4451,130
Succinylation17,5965,18422,78062
Methylation17,48318,03635,5198,806
Malonylation8,7361378,87314
N-linked Glycosylation7,916103,976111,8921,842
O-linked Glycosylation6,3401,6267,9663,785
Sumoylation5,4509,94315,393178
S-nitrosylation4,2034734,676324
Glutathionylation4,161444,20592
Amidation2,9071,2964,203896
Palmitoylation1,0946,7667,860382
Hydroxylation1,7252,7844,509285
Pyrrolidone carboxylic acid9087121,620529
Glutarylation767458123
Gamma-carboxyglutamic acid4397481,18787
Crotonylation3682686366
Oxidation35933669524
Myristoylation2791,4281,707182
C-linked Glycosylation25510435917
Sulfation2511,1281,379120
Formylation2503328340
Citrullination12235147319
GPI-anchor829721,05447
Nitration7724832515
S-diacylglycerol572,0732,13048
Carboxylation401,5051,54538
Lipoylation3556660129
Carbamidation220221
Neddylation110114
Pyruvate91,6361,6456
S-linked Glycosylation66125
Pyrrolylation04694690
Total in dbPTM908,917347,9841,256,90192,648

Data statistics of benchmark dataset for nine PTM types with sufficient data - [Go to the Download page]

PTM TypeNumber of ProteinsNumber of Positive sitesNumber of Negative sites
Phosphorylation by AKT35138014,617
Phosphorylation by DMPK991093,533
Phosphorylation by GRK771472,310
Phosphorylation by NDR28321,096
Phosphorylation by PDK177932,274
Phosphorylation by PKA9051,20929,813
Phosphorylation by PKC69194324,207
Phosphorylation by PKG1261457,311
Phosphorylation by PKN2650866
Phosphorylation by RSK2212156,985
Phosphorylation by SGK63773,057
Acetylation40,996109,6761,589
Carbamidation1920411
Citrullination67761,501
C-linked Glycosylation22197331
Crotonylation6911736
Formylation1591721,452
Gamma-carboxyglutamic acid110319553
Glutarylation2107252,543
Glutathionylation2,3373,5556,617
Hydroxylation3851,2732,876
Lipoylation2829779
Malonylation3,3198,11916,625
Methylation7,01714,68636,502
Nitration6166982
N-linked Glycosylation28,38986,1831,894
O-linked Glycosylation1,3455,24950,373
S-diacylglycerol575759
S-nitrosylation2,3023,5925,803
Succinylation6,32016,0255,505
Sumoylation1799,590130,649
Ubiquitination27,86146,8864,901

The statistics of external PTM resource in dbPTM

ResourceVersionNumber of PTM sitesNumber of experimental PTM SitesNumber of putative sitesNumber of Literatures
ProteomeScoutRelease 2018_05704,38715,62740688,760
SysPTMRelease 2.0514,76641,3401,352473,426
dbPAFRelease 1.0483,001483,00115,1390
PhosphoSitePlusRelease 2018_05428,47685,13679,935343,340
ActiveDriverDBRelease 1.0385,186368,0053,68217,181
UniProtKBRelease 2018_03373,81597,17210,080276,643
CPLMRelease 2.0203,97200203,972
PLMDRelease 3.0184,779184,4171,590362
SubPhosDBRelease 2013_07137,15300137,153
mUbiSiDaRelease 2013_10111,208111,2081020
HPRDRelease 9.093,71049,8111,83243,899
UbisiteRelease 1.092,43291,58824,988844
PHOSIDARelease 3.6980,06280,062170
dbPPTRelease 1.069,29769,297790
Phospho.ELMRelease 9.050,66050,6223,58938
UbiNetRelease 1.044,17544,1752330
PhosphoGRIDRelease 2.042,90842,9085280
ESBLRelease 2018_0520,0019,970510,031
dbPSPRelease 1.07,391007,391
SwissPalmRelease 2.05,3845,3844250
ASEBRelease 2015_124,8754,8752810
CarbonylDBRelease 2018_054,1984,19811213
dbSNORelease 2.04,1654,1611754
dbGSHRelease 1.04,1194,119600
OGlycBaseRelease 6.02,2212,21117810
ProteomeXchangeRelease 2018_0553946424375
Mal-LysRelease 1.048300483
MeMoRelease 2.0364364570
PupDBRelease 1.33111954116
PredGPIRelease 1.0260026
dbPTMRelease 20191,256,901908,917347,98492,648

The statistics of non-synonymous SNPs (nsSNPs) altering PTM sites in Human

Data CategoryDescriptionResourceNumber of Data
Experimental PTM SitesThe experimental PTM sites in human are integrated by dbPTM.dbPTM 2019438,624
Protein VariantsThe natural variants were annotated, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events.UniProtKB79,164
Protein Variants with SNP AnnotationValidated human polymorphisms from the NCBI dbSNP database are annotated to protein entries of UniProt.dbSNP59,555
Disease-associated SNPsAll published GWA studies are identified by literature search,then extract the reported trait, significant SNP-trait associations.GWAS Catalog71,370
SNP influencing PTM Sites (SNP-PTM)To investigated the PTM sites related to single nucleotide polymorphism, which linking the UniProt ID of experimental PTM dataset to the protein variants with SNP annotation.42,245
Disease-associated SNP-PTM SitesMerging the SNP-PTM dataset and disease-associated SNPs for discovery of disease-associated single nucleotide polymorphism influencing PTM sites.1,141

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