ABCatlas — Data Repository

Comparative functional knowledgebase of ABC transporters in Homo sapiens (48 proteins) and Saccharomyces cerevisiae (31 proteins). Integrates six feature dimensions — subfamily classification, substrate specificity, subcellular localisation, structural similarity (TM-align), orthology confidence, and disease burden — into a single annotation framework.

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Repository Structure

abcatlas_data/
├── raw/          Source data retrieved from public databases
└── processed/    Analysis outputs used in all figures and statistics

raw/

File	Source	Description
uniprot_human_abc.tsv	UniProt	Human ABC transporter annotations (48 proteins)
uniprot_yeast_abc.tsv	UniProt	Yeast ABC transporter annotations (31 proteins)
uniprot_human_domains.tsv	UniProt	Domain architecture — human
uniprot_yeast_domains.tsv	UniProt	Domain architecture — yeast
uniprot_human_go.tsv	UniProt/GO	GO term assignments — human
uniprot_yeast_go.tsv	UniProt/GO	GO term assignments — yeast
gtex_human_tissue_expression.tsv	GTEx v8	Median TPM across 54 human tissues
hpa_localization.json	Human Protein Atlas	Subcellular localisation — human
clinvar_counts.tsv	ClinVar	Pathogenic/likely-pathogenic variant counts per gene
panther_human_yeast_orthologs.tsv	PANTHER 18.0	Human–yeast orthology assignments with confidence scores
sgd_phenotypes.json	SGD	Yeast phenotype and stress-response data
alphafold_metadata.json	AlphaFold DB v4	Structure model metadata (pLDDT, coverage)

processed/

File	Description
master_annotation_table.tsv	Core table: 79 proteins x 48 columns, all feature dimensions merged
master_gene_list.tsv	Protein identifiers, gene names, organisms, and subfamily assignments
feature_matrix.tsv	Normalised feature vectors used as UMAP input
landscape_coordinates.tsv	UMAP embeddings and HDBSCAN cluster assignments (5 clusters)
structural_similarity_tmscore_matrix.tsv	All-versus-all TM-scores (3,081 pairs; 79 x 79)
structural_comparison_ortholog_pairs.tsv	TM-scores and structural metadata for confirmed ortholog pairs
orthology_map.tsv	Human–yeast ortholog pairs with PANTHER confidence tiers
orthology_comparative_analysis.tsv	Substrate Jaccard indices by orthology confidence group
substrate_annotation.tsv	Manually curated substrate class assignments
localization_matrix.tsv	Binary subcellular compartment matrix (HPA + SGD)
expression_summary.tsv	Tissue expression profiles — human (GTEx)
disease_phenotype_summary.tsv	OMIM disease associations and ClinVar variant counts
variation_summary.tsv	Variant burden summary per protein
annotation_completeness_matrix.tsv	Per-feature annotation completeness scores; flags one-sided gaps
yeast_stress_response_summary.tsv	Stress response rates across 13 conditions (SGD)
structure_quality.tsv	AlphaFold pLDDT scores and coverage per protein
validation_mannwhitney_summary.tsv	Mann–Whitney U test results for orthology–substrate analysis
validation_permutation_summary.tsv	Permutation test summary statistics
validation_substrate_jaccard_groups.tsv	Per-pair Jaccard scores used in validation

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Methods Summary

Dimensionality reduction: UMAP (n_neighbors=15, min_dist=0.1) on a six-dimension normalised feature matrix. Clustering: HDBSCAN (min_cluster_size=6). Structural comparisons: TM-align run on all 3,081 pairwise combinations of AlphaFold models. Orthology confidence tiers (High / Medium / Low) derived from PANTHER 18.0 scores. All analysis performed in Python 3.11 and R 4.5.

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Citation

Harrzi Saad A. ABCatlas: a comparative functional knowledgebase of ABC transporters in Homo sapiens and Saccharomyces cerevisiae. 2026. Preprint / in review.

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Licence

Creative Commons Attribution 4.0 International (CC BY 4.0). See LICENSE for full terms.