pMHC Data Compendium — Data Catalog

Harmonized public data for a personalized cancer-vaccine immunogenicity pipeline: epitope–MHC presentation, immunogenicity labels, thymic & proteomic self references, foreign ligandomes, and HLA population frequencies. Per-patient cohort data is private and excluded here.

datasets

7,423,658

records

5,263,507

distinct peptides

sources

tissues / origins

downstream tools

Records by category

Immunogenicity4,917,562

Presentation2,127,683

Self reference266,734

Foreign reference104,508

HLA frequencies7,171

Peptide–MHC records by species

Human7,084,713

Mouse291,226

Peptide–MHC records by MHC class

MHC class I6,456,191

MHC class II717,385

Records by tissue / origin

Tumor4,127,087

Viral88,041

Thymus64,371

Microbial / viral16,467

Population7,171

Datasets per downstream tool

mhcmatch3 ds

ipred2 ds

public-epitope1 ds

seqtree7 ds

model4 ds

Datasets per source

IEDB4 ds

UniProt3 ds

NCI2 ds

HLA Ligand Atlas2 ds

TESLA1 ds

CEDAR1 ds

Gfeller1 ds

ITSNdb1 ds

GBM1 ds

VACCIMEL1 ds

Bjerregaard1 ds

TCGA1 ds

AFND1 ds

HPA1 ds

GSE2724061 ds

tsarina1 ds

Dataset	Category	Species	MHC	Records	Distinct peptides	Tissue	Source	Feeds
IEDB epitope–MHC	Presentation	human+mouse	I+II	1,482,188	689,421	—	IEDB	mhcmatch
IEDB epitope–MHC (≥2 refs)	Presentation	human+mouse	I+II	645,102	174,821	—	IEDB	mhcmatch
IEDB immunogenicity	Immunogenicity	human+mouse	I+II	790,868	516,092	—	IEDB	ipred, public-epitope
Neoantigens — tested	Immunogenicity	human	I+II	525,989	491,495	Tumor	TESLA, NCI, CEDAR, Gfeller, ITSNdb, GBM, VACCIMEL, Bjerregaard	model, ipred
Neoantigens — candidates	Immunogenicity	human	I	1,355,926	1,344,070	Tumor	NCI	model
TCGA neoantigens	Immunogenicity	human	I	2,244,779	1,948,737	Tumor	TCGA	model
HLA population freqs	HLA frequencies	—	—	7,171	—	Population	AFND	model
Thymus self-peptidome	Self reference	human	I+II	53,878	53,878	Thymus	HLA Ligand Atlas	seqtree
Thymus expression	Self reference	—	—	10,493	—	Thymus	HPA, HLA Ligand Atlas	seqtree
Human proteome	Self reference	human	—	147,506	—	—	UniProt	seqtree
Mouse proteome	Self reference	mouse	—	54,857	—	—	UniProt	seqtree
Bacterial + viral proteomes	Foreign reference	foreign	—	16,467	—	Microbial / viral	UniProt	seqtree
Viral ligandome (IEDB)	Foreign reference	human+mouse	I+II	82,368	44,993	Viral	IEDB	seqtree
Pan-viral ORFs (GSE272406)	Foreign reference	—	—	5,673	—	Viral	GSE272406	seqtree
Cancer-testis antigens	Presentation	—	—	393	—	Tumor	tsarina	mhcmatch

Generated by pipeline/build_catalog.py from the public compendium. Immunopeptidome self-reference (thymus) from the HLA Ligand Atlas (Marcu 2021, CC-BY 4.0); proteomes from UniProt; HLA frequencies from AFND. See DESCRIPTION.md for provenance.