expression/SOURCES.md

expression/ — sources

One file, three references that are never merged — different measurements, different units, and a gene-keyed table and a peptide-keyed one are not the same object.

file	reference_expression.tsv.gz
rows	6,681,814
schema	key, key_type, source, context, median_tpm, q25_tpm, q75_tpm, n
provenance	experimental (all three sources are measured RNA-seq); the per-context median/IQR/n are computed summaries of it

source	key_type	rows	contexts	what a row is
gtex	gene	3,955,284	53	a gene's expression across normal tissue — the safety read
hpa_consensus	gene	1,025,751	51	the same read over HPA's tissue panel — the only one that contains thymus
tcga	peptide	1,700,779	19	a mutant peptide's expression by tumour type — the target read

Total 6,681,814 rows.

key_type is the join key and it differs by source on purpose: GTEx and HPA answer "is this gene on in normal tissue", TCGA answers "is this neoantigen transcribed in this tumour". A caller that treats them as one column is asking a question none of them answers. GTEx and HPA are both gene-keyed but are still not interchangeable — see the units caveat in the HPA section below.

Read through mhcmatch.expression (lookup, tissues, tumor_types, safety_profile), which keeps them apart. Fetched by mhcmatch bootstrap --reference (~115 MB).

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Mouse — reference_expression_mmu.tsv.gz and protein_abundance_mmu.tsv.gz

Added 2026-08-21. The compendium's normal-tissue safety read was GTEx, and GTEx is human, so a mouse epitope had no reference to be scored against. These two files are the mouse counterpart.

They are two files, not one, and that is deliberate. The human table's value column is literally median_tpm. RNA and protein are different measurements in different units, and writing a SILAC abundance into a _tpm column would be a units lie no caller could detect.

reference_expression_mmu.tsv.gz — the GTEx analogue

rows	659,050
schema	key, key_type, source, context, median_tpm, q25_tpm, q75_tpm, n — column for column identical to the human file
keys	18,830 gene symbols (key_type = gene)
contexts	35 adult tissues
source	fantom5_mouse
provenance	experimental — CAGE tag counts; the per-gene median across transcripts and the quantile summary are computed

Origin. EBI Expression Atlas E-MTAB-3579, the RIKEN FANTOM5 mouse CAGE atlas. q25_tpm / median_tpm / q75_tpm are taken from the Atlas' own five-number summary per gene × group; they are not re-derived here.

Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PAC, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest ARR, Kawaji H. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol 2015;16:22. PMID 25723102 · doi:10.1186/s13059-014-0560-6

Only plain adult groups are kept — 35 of the deposit's 170. GTEx is adult normal tissue; folding an E14 embryo, a pregnancy timepoint or a lactating mammary gland into a "is this gene on in normal tissue" safety read answers a different question. The other stages are in the source and are recoverable by re-running without the filter.

A parsing trap worth recording. Atlas group labels are two ;-separated parts and the order is not fixed: 136 of the 170 are stage-first (adult; thymus) and 32 are tissue-first (adrenal gland; adult). Taking either position blindly mislabels a third of the table — the first build of this file produced contexts named adult and whole body that way. The stage is matched by vocabulary wherever it sits, and the tissue is whatever remains.

Checked against known biology, not assumed. Of 35 tissues, thymus ranks first for Prss16 (31 TPM), Psmb11 (88), Dntt (961), Rag1, Cd8a (131) and Lck (12) — thymic epithelium and thymocyte genes. As a negative control Cela1 peaks in pancreas at 225,010 TPM against 0.3 in thymus.

Caveats.

• n is 1 for every row. FANTOM5 provides one library per adult tissue, so q25/q75 describe the spread across transcripts of a gene, not across animals. GTEx n runs to several hundred donors. Do not read the two n columns as the same quantity.
• Aire is 0 TPM in thymus here, and that is a detection floor, not biology. Aire is expressed in a rare mTEC subset; bulk CAGE at this depth cannot see it. Any promiscuous-expression question needs sorted mTEC data, not this file.
• CAGE measures 5′-capped tag density. It is reported as TPM and behaves like expression, but it is not RNA-seq TPM and the two are not numerically interchangeable across sources.

protein_abundance_mmu.tsv.gz — the protein-level read

rows	133,848
schema	key, key_type, source, context, abundance, unit, n
keys	5,148 gene symbols
contexts	26 tissues, including thymus
source / unit	geiger_silac_mouse / ppb_ibaq
provenance	experimental — SILAC-normalised MS abundance

Origin. EBI Expression Atlas E-PROT-11.

Geiger T, Velic A, Macek B, Lundberg E, Kampf C, Nagaraj N, Uhlen M, Cox J, Mann M. Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Mol Cell Proteomics 2013;12(6):1709–1722. PMID 23436904 · doi:10.1074/mcp.M112.024919

Why keep a protein table at all. A peptide can only be presented if the protein was translated, so for immunopeptidome work protein abundance is the more direct evidence and RNA is a proxy. It is much shallower — 5,148 genes against 18,830 — so it complements the RNA table rather than replacing it.

Why not E-PROT-13

E-PROT-13 (Huttlin's mouse phosphorylation and expression atlas) was the first candidate considered. It covers 9 tissues and does not include thymus, so it cannot serve either purpose here. Of the 65 mouse baseline experiments in Expression Atlas, only six contain thymus; E-MTAB-3579 (35 adult tissues) and E-PROT-11 (26) are the only two of those with broad tissue coverage.

Regenerate

cd ~/vcs/projects/2026-mouse-thymus && ./src/build_expression_mmu.py

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Human — the hpa_consensus arm, and why GTEx alone was not enough

Added 2026-08-21, in the same pass that built the mouse references.

GTEx has no thymus. Its 53 contexts contain no thymus, no lymph node and no bone marrow — adult thymus involutes and is not routinely sampled, so the normal-tissue safety read was blind to the one tissue central tolerance actually happens in. Expression Atlas is no better: of its 123 human baseline experiments only three carry any thymus group, and all three are compromised for this purpose — E-MTAB-3871 is fetal tissue from fetuses with congenital defects, E-MTAB-3827 is sorted thymocyte subsets rather than tissue, and E-MTAB-9641 is thymic epithelium cultured on a 3T3-J2 feeder layer.

HPA samples thymus directly, so its consensus tissue set is what fills the hole.

rows	1,025,751
keys	20,151 gene symbols (key_type = gene)
contexts	51 tissues, including thymus
source	hpa_consensus
provenance	experimental — RNA-seq; the HPA consensus normalisation is computed

Origin. rna_tissue_consensus.tsv.zip from the Human Protein Atlas.

Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Tissue-based map of the human proteome. Science 2015;347(6220):1260419. PMID 25613900 · doi:10.1126/science.1260419

It is added as a third source, not merged into GTEx and not replacing it. The schema was designed with a source column for exactly this; every existing gtex and tcga row is untouched.

Checked against known biology. Of 51 tissues, thymus ranks first for PRSS16 (770 nTPM), PSMB11 (28.5), DNTT (306), CD1A (296), RAG1 (368), CCL25 (718), CD3E (596) and LCK (326). Negative controls behave: ALB peaks in liver at 198,524 nTPM against 0.3 in thymus, INS in pancreas, MYH7 in skeletal muscle.

Caveats.

• nTPM is not GTEx TPM. Both are TPM-family units but the normalisation differs, so compare within a source, not across. This is what the source column is for.
• n is 1 — HPA consensus publishes one value per gene × tissue, so q25_tpm and q75_tpm equal median_tpm and carry no spread. GTEx n runs to several hundred donors; the two n columns are not the same quantity.
• AIRE is detectable here (1.2 nTPM, rank 2 of 51) but reads 0 in the mouse CAGE atlas. That is a difference in assay depth, not in biology — do not read it as a species difference.