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).

---

## 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](https://www.ebi.ac.uk/gxa/experiments/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](https://pubmed.ncbi.nlm.nih.gov/25723102/) ·
> doi:[10.1186/s13059-014-0560-6](https://doi.org/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](https://www.ebi.ac.uk/gxa/experiments/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](https://pubmed.ncbi.nlm.nih.gov/23436904/) ·
> doi:[10.1074/mcp.M112.024919](https://doi.org/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](https://www.ebi.ac.uk/gxa/experiments/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

---

## 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`](https://www.proteinatlas.org/download/tsv/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](https://pubmed.ncbi.nlm.nih.gov/25613900/) ·
> doi:[10.1126/science.1260419](https://doi.org/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.