ingenix/mapping_benchmark

Mapping benchmark

A collection of harmonized gene-expression datasets, somatic mutation tables and a MONDO disease hierarchy for benchmarking the matching of biological models to patient tumour profiles.

The collection brings together patient samples, patient-derived xenografts (PDXs) and cancer cell lines. Expression datasets share a 19,260-gene reference panel, and disease descriptions were mapped to MONDO by our team using metadata supplied by the original authors.

Component	Contents	Format
Expression	Five datasets with TPM values, sample metadata and MONDO labels	AnnData / H5AD
Mutations	Gene-level mutation presence and sample/gene reference tables for TCGA, META-PRISM and DepMap	Parquet
Disease hierarchy	15,481 MONDO terms and 25,555 parent relations	Parquet

Expression datasets

Each H5AD contains a sample-by-gene matrix. All five datasets use the same ordered gene panel.

Dataset	Biological material	Samples	Genes	Zero-padded genes	File
PDXE	Patient-derived xenografts	357	19,260	315	pdxe_tpm.h5ad
META-PRISM	Metastatic patient tumours	932	19,260	79	metaprism_tpm.h5ad
TCGA	Patient tissue samples	11,425	19,260	29	tcga_tpm.h5ad
DepMap 24Q4	Cancer cell lines	1,508	19,260	285	depmap_tpm.h5ad
GSE317901	Head-and-neck cancer patient/PDX samples	114	19,260	106	gse317901_tpm.h5ad

What is stored in each H5AD?

Field	Description
X	Gene-expression values in TPM, stored as a sparse matrix
obs_names	Sample identifiers used to join expression and mutation data
obs["ontology_disease_matched_id"]	MONDO disease identifiers added by our team
obs["ontology_disease_matched_name"]	Corresponding disease names added by our team
obs	Selected source-derived tissue, histology and disease descriptors; available fields vary by dataset
var_names	Harmonized Ensembl gene identifiers
var["artificial_gene"]	Boolean flag identifying genes appended to complete the common panel

Zero padding: genes missing from a dataset's standardized gene set were added with all-zero expression and artificial_gene=True. A value of False means that the gene was already present; it does not guarantee nonzero expression.

Preparation

Gene harmonization. Gene identifiers were standardized. Genes were filtered against a common reference panel of 19,260 genes. Genes outside the reference panel were excluded. Missing panel genes were appended with zeros, and the final columns were sorted by Ensembl identifier.

Expression processing. For PDXE, human transcript TPM values were aggregated to genes and rescaled to one million per sample over the selected panel. META-PRISM TPM measurements were matched to clinical records. TCGA used GDC unstranded gene TPM values. DepMap 24Q4 log2(TPM+1) values were converted back to TPM. GSE317901 TPM measurements were associated with patient/PDX sample metadata.

Disease annotation. MONDO labels were added by our team based on the authors' metadata columns. Samples without a validly formatted MONDO identifier were excluded. Expression values in the final export were preserved from the corresponding standardized matrices.

Mutation data

Three complementary tables connect mutation data directly to the expression samples. The dataset column contains tcga, metaprism or depmap.

File	One row represents	Columns	Rows
mutated_genes.parquet	A sample–gene pair with a qualifying mutation	dataset, sample_id, gene_id_ensembl, gene_symbol	345,620
assayed_samples.parquet	An expression sample represented in the mutation matrices	dataset, sample_id	10,696
assayed_genes.parquet	A gene represented in a dataset's mutation matrix	dataset, gene_id_ensembl	37,298

Dataset	Samples with mutation data	Mutated sample–gene pairs	Genes in the mutation matrix
TCGA	8,877	244,203	18,566
META-PRISM	354	567	124
DepMap	1,465	100,850	18,608

Mutation definition Variants with vep_impact equal to HIGH or MODERATE were retained. Multiple qualifying variants in a gene were collapsed to binary presence. These tables describe mutation presence, rather than individual variants or allele frequencies.

Sample matching Join by dataset and sample_id; sample_id matches the observation identifier in the corresponding H5AD. TCGA patient-level calls and META-PRISM subject-level calls were assigned to their expression samples. DepMap calls were matched to model identifiers. DepMap mutation data use 25Q3, while expression data use 24Q4.

Missing data A sample present in assayed_samples but absent from mutated_genes has no qualifying mutation in the represented gene set. A sample absent from assayed_samples has no mutation data in this export.

Comparison panel The intersection of the three mutation gene sets contains 124 genes. The assayed_genes table records columns present in the input mutation matrices.

MONDO disease hierarchy

mondo_ontology/train-00000-of-00001.parquet contains 15,481 terms, 25,555 parent relations and ten columns.

Columns	Description
mondo_id, name	Disease identifier and name
mondo_level	Minimum distance from the root
parent_mondo_id	One selected direct parent, provided for convenience
direct_ancestors_ids, direct_ancestors_names, len_direct_ancestors	All direct parents and their count
all_ancestors_ids, all_ancestors_names, len_all_ancestors	Ancestors and their count

Use direct_ancestors_ids when reconstructing the graph, because terms may have more than one parent.

The non-human animal disease branch (MONDO:0005583 and 62 exclusive descendants) was removed. The resulting graph is acyclic and has one root, MONDO:0000001.

Sources and attribution

Component	Original source
PDXE expression	NIBR; Gao et al., Nature Medicine (2015), doi:10.1038/nm.3954; PDXE data deposit
META-PRISM expression	Gustave Roussy; META-PRISM processed data
TCGA expression	NCI/NHGRI; Genomic Data Commons
DepMap expression	Broad Institute; DepMap 24Q4 Public
GSE317901 expression	Queen's University Belfast and collaborators; GEO GSE317901
TCGA mutations	cBioPortal Datahub, *tcga_pan_can_atlas_2018*/data_mutations.txt
META-PRISM mutations	Publication supplementary material, Table S6
DepMap mutations	Broad Institute; DepMap Public 25Q3, OmicsSomaticMutations.csv
MONDO	Monarch Initiative; Mondo Disease Ontology; official OBO reference

Licence and reuse

Source-specific licences and attribution requirements apply. The collection does not assign a single licence to all components.

The PDXE deposit, DepMap 24Q4 expression release and MONDO ontology identify CC BY 4.0. META-PRISM processed expression tables were made publicly available by the authors. TCGA expression was obtained through GDC open-access resources. GEO data are subject to NCBI's data-use notice.