PTMcosmos

About PTMcosmos

PTMcosmos is a database that stores post-translational modifications (PTMs) and cancer mutations in humans. It keeps track of supporting evidence for PTMs, which include previous publications, experimental validation and manual curations. It also stores Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomics data, which provides multi-omic profiles from DNA sequencing to protein and PTM mass spectrometry data from cancer and their paired normal samples. Combining PTM and mutation information, PTMcosmos enables users to explore the potential disruption of a PTM function by overlapping or nearby mutations in cancer.

We hope PTMcosmos will serve CPTAC and general research community to better understand the role of PTMs in cancer.

Downloads (under construction)

A snapshot of all PTM sites and their number of supporting evidence is released roughly every month. Please refer to the Downloads page.

Development team

Liang-Bo Wang
Akshay Govindan

Funding

PTMcosmos is supported by CPTAC and TCGA grants and institutional support.

Data sources

PTMcosmos was built based on the following data sources:

Human genome: GRCh38
Gene information from HGNC: Snapshot on 2021-04-01
Protein information from UniProt Knowledge Base: Release 2021.02
PTM information from PhosphoSitePlus: v6.5.9.3 snapshot on 2021-04-19
TCGA MC3 somatic mutations: Version 0.2.8
CPTAC experimental data (see below)

CPTAC experimental data

Visit this repository for the details of CPTAC proteome data preprocessing.

Notes for the peptide databases (bold ones are commonly used):

RefSeq 20111201: CDAP (RefSeq release 37); Incomplete annotation; hg19

RefSeq 20130727: Incomplete annotation; hg19

RefSeq 20171003: Currently overwrite the annotation using RefSeq 20180629; hg38

**RefSeq 20160914**: CDAP (Refseq 2016); hg19

**RefSeq 20180629**: CDAP (RefSeq 2018); hg38

RefSeq 20180629*: database includes smORFs
Cohort	Global	Phospho	Acetyl	Ubiquityl	Peptide database
TCGA_BRCA_retrospective	v	v	-	-	RefSeq 20130727
TCGA_OV_retrospective	v	v	-	-	RefSeq 20111201
CPTAC2_BRCA_prospective	v	v	v	-	RefSeq 20160914
CPTAC2_CRC_prospective	v	v	-	-	RefSeq 20171003
CPTAC2_OV_prospective	v	v	-	-	RefSeq 20160914
CPTAC3_CCRCC_discovery	v	v	-	-	RefSeq 20180629
CPTAC3_HNSCC_discovery	v	v	-	-	RefSeq 20180629
CPTAC3_LUAD_discovery	v	v	v	-	RefSeq 20180629*
CPTAC3_LSCC_discovery	v	v	v	v	RefSeq 20180629*
CPTAC3_GBM_discovery	v	v	v	-	RefSeq 20180629
CPTAC3_UCEC_discovery	v	v	v	-	RefSeq 20180629

License

HGNC

No restrictions are imposed on access to, or use of, the data provided by the HUGO Gene Nomenclature Committee at the European Bioinformatics Institute.

Ensembl

Ensembl data are available without restriction. Reference: Ensembl 2017. Bronwen L. Aken, Premanand Achuthan, Wasiu Akanni, et al. Nucleic Acids Res. 45:D635-D642. (2017) [PubMed] [Europe PMC]

UniProt

The database is released under Creative Commons Attribution (CC BY 4.0) License. Reference: UniProt: the universal protein knowledgebase. The UniProt Consortium. Nucleic Acids Res. 45:D158-D169 (2017) [PubMed] [Europe PMC]

PhosphoSitePlus

PhosphoSitePlus (PSP) is licensed by Cell Signaling Technology under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0) License. Reference: PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. Nucleic Acids Res. 43:D512-20 (2015) [PubMed] [Europe PMC]

TCGA MC3

Reference: Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Kyle Ellrott, Matthew H Bailey, Gordon Saksena, et al. Cell Systems 6:271-281.e7 (2018) [PubMed] [Europe PMC]