expression: the mouse normal-tissue reference, and the thymus slice of it

GTEx is human, so a mouse epitope had no normal-tissue safety read to be scored
against. Three files close that, plus the mouse thymus expression gap that
thymus/SOURCES.md recorded as open.

expression/reference_expression_mmu.tsv.gz 659,050 rows / 18,830 genes / 35 adult tissues
expression/protein_abundance_mmu.tsv.gz 133,848 rows / 5,148 genes / 26 tissues
thymus/thymus_expression_mmu.tsv.gz 15,306 rows / 12,646 genes

The RNA file is column for column identical to the human one. RNA and protein are
deliberately NOT merged: the human value column is named median_tpm, and writing a
SILAC abundance into it would be a units lie no caller could detect.

E-PROT-13 was the starting suggestion and is not used: 9 tissues, no thymus. Of the
65 mouse baseline experiments in Expression Atlas only six contain thymus at all, and
E-MTAB-3579 (FANTOM5 CAGE, 35 adult tissues) and E-PROT-11 (Geiger SILAC, 26) are the
only broad ones among them.

Checked rather than assumed: of 35 tissues thymus ranks first for Prss16, Psmb11,
Dntt (961 TPM), Rag1, Cd8a and Lck, while Cela1 peaks in pancreas at 225,010 TPM
against 0.3 in thymus.

Two traps recorded in SOURCES.md. Atlas group labels are two semicolon-separated parts
whose order is NOT fixed -- 136 of 170 are stage-first, 32 tissue-first -- and taking
either position blindly produced contexts named `adult` and `whole body` on the first
pass. And Aire reads 0 TPM in whole thymus: it is confined to a rare mTEC subset, so
this is a detection floor and the promiscuous-expression question still needs sorted
mTEC data.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

DESCRIPTION.md

@@ -57,6 +57,14 @@ the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive and the mTEC-T
 (Sansom GSE53111) is journal-supplement-only. See `thymus/SOURCES.md` for the per-deposit FDR
 regimes, which differ and are not interchangeable.
 
+**The normal-tissue safety read is no longer human-only either.** GTEx has no mouse counterpart, so
+a mouse epitope had nothing to be scored against. `expression/reference_expression_mmu.tsv.gz`
+(2026-08-21) is that counterpart — 18,830 genes across 35 adult tissues from the FANTOM5 mouse CAGE
+atlas, column for column identical to the human file — with `expression/protein_abundance_mmu.tsv.gz`
+as the protein-level read and `thymus/thymus_expression_mmu.tsv.gz` as the thymus slice of both. RNA
+and protein are deliberately **not** merged: the human value column is named `median_tpm`, and a
+SILAC abundance is not a TPM.
+
 ## Public datasets (this repo)
 
 Per-directory provenance, filtering procedures, verified PubMed citations and complete
@@ -102,6 +110,9 @@ Every tracked directory now carries one:
 | `ligandome/viral_orfs_gse272406.tsv.gz` | Pan-viral ORFs (GSE272406) | translated novel viral ORF proteins (foreign; *not* thymus self — spec mislabel) |
 | `ligandome/cancer_targets_tsarina.tsv.gz` | Cancer-testis antigens | curated shared tumor-antigen genes (tsarina) |
 | `ligandome/tissue_self_mmu.tsv.gz` | Tissue self-ligandome (mouse) | 46,334 rows / 17,256 distinct peptides across **18 non-thymic tissues**, Schuster murine MHC-I atlas (PXD008733) at a recomputed 1% peptide FDR. H-2Kb 8,829 + H-2Db 7,781 peptides (MHC-I) and 4,348 I-Ab (MHC-II); carries a `tissue` column. Tumour cell lines (EL4, B16F10, GL261, LLC) excluded — they are not normal tissue |
+| `expression/reference_expression_mmu.tsv.gz` | Reference expression (mouse) | 659,050 rows / 18,830 genes across **35 adult tissues**, `source=fantom5_mouse`. Column for column identical to the human file — the mouse GTEx analogue, the normal-tissue safety read for a mouse epitope. FANTOM5 CAGE (E-MTAB-3579). `n`=1 per tissue: the IQR is across transcripts, not animals |
+| `expression/protein_abundance_mmu.tsv.gz` | Protein abundance (mouse) | 133,848 rows / 5,148 genes across 26 tissues, `source=geiger_silac_mouse`, `unit=ppb_ibaq` (E-PROT-11). Kept apart from the RNA table on purpose — a SILAC abundance is not a TPM |
+| `thymus/thymus_expression_mmu.tsv.gz` | Thymus expression (mouse) | 15,306 rows / 12,646 genes: adult-thymus CAGE TPM (11,862) + thymus SILAC protein (3,444). `value` carries the measurement so callers can threshold. `Aire` reads 0 — a detection floor, not biology |
 | `summary.tsv` | Pipeline stats | row counts & extraction metrics |
 
 ## Private (gitignored — NOT in this repo)

expression/SOURCES.md

@@ -21,3 +21,101 @@ them as one column is asking a question neither answers.
 
 Read through `mhcmatch.expression` (`lookup`, `tissues`, `tumor_types`, `safety_profile`), which
 keeps the two apart. Fetched by `mhcmatch bootstrap --reference` (~105 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

expression/protein_abundance_mmu.tsv.gz

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+size 1206843

expression/reference_expression_mmu.tsv.gz

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thymus/SOURCES.md

@@ -113,6 +113,22 @@ Twelve of the deposit's 37 runs — the four thymus samples (`120116WTII`, `0206
 dendritic-cell arms and the human LCL runs are deliberately **not** included: this is a thymic
 reference, and pooling peripheral APCs into it would destroy the distinction the file exists to make.
 
+## `thymus_expression_mmu.tsv.gz` — 15,306 rows
+
+The mouse side of the table below, added 2026-08-21. Schema `gene`, `species`, `evidence`, `value`;
+`species = MusMusculus` throughout, and unlike the human file `value` is populated — it carries the
+measurement, so a caller can threshold rather than take mere presence as evidence.
+
+| `evidence` | rows | what it is |
+|---|--:|---|
+| `fantom5_mouse_thymus_tpm` | 11,862 | adult-thymus CAGE median TPM > 0 (E-MTAB-3579) |
+| `geiger_silac_thymus_ppb` | 3,444 | thymus SILAC protein abundance > 0 (E-PROT-11) |
+
+12,646 distinct genes. The two lines of evidence are kept in a column rather than pooled, exactly as
+in the human file: one says the gene is transcribed in thymus, the other that its protein was
+detected there. Full provenance, citations and caveats — including why `Aire` reads zero — are in
+`expression/SOURCES.md`.
+
 ## `thymus_expression.tsv.gz` — 10,493 rows
 
 Thymically expressed self, by gene. Schema: `gene`, `species`, `evidence`, `value`.
@@ -143,10 +159,12 @@ support each other; they are not interchangeable. Human only — there is no mou
 
 ## Not here
 
-**No mouse thymus *expression* table.** The mTEC-TRA gene list (Sansom, GSE53111) is
-journal-supplement-only, and the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive.
-`thymus_expression.tsv.gz` stays human-only until one of those is processed — **absent, not
-overlooked**.
+**The mouse thymus expression gap is closed** — see `thymus_expression_mmu.tsv.gz` above. What
+is still absent is a *promiscuous-expression* (AIRE-driven TRA) table: the Sansom mTEC-TRA gene list
+(GSE53111) is journal-supplement-only and the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant
+archive. Bulk data cannot substitute — `Aire` itself reads 0 TPM in whole thymus because it is
+confined to a rare mTEC subset, so the promiscuous-expression question needs sorted mTEC, not this
+file. **Absent, not overlooked.**
 
 **PXD031966 is not here, and that is a labelling problem rather than a data problem.** The NOD-mouse
 MHC-I deposit covers thymus *and* pancreas, but its experiment labels (`ICR1`, `ICR6`, `NOD2_3`,

thymus/thymus_expression_mmu.tsv.gz

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