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Curated and harmonised transcriptomics datasets of interstitial lung diseases
Simo Inkala1, Antonio Federico1,2,3, Angela Serra1,2,3
1Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100, Tampere, Finland.
Data in Brief
|November 5, 2025
Summary
This study presents a curated transcriptomics data compendium for interstitial lung disease (ILD) patients, integrating 30 datasets for enhanced analysis. The resource facilitates systems biology approaches for novel diagnostic and therapeutic strategies in ILD.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Interstitial lung disease (ILD) encompasses a heterogeneous group of disorders with significant unmet clinical needs.
- Publicly available transcriptomics data for ILD are often fragmented across repositories, hindering comprehensive analysis.
- Existing datasets lack standardized formats and quality control, limiting their interoperability and reusability.
Purpose of the Study:
- To create a manually curated and harmonized transcriptomics data compendium for interstitial lung disease (ILD) patients.
- To enhance the Findability, Accessibility, Interoperability, and Reusability (FAIR) of ILD transcriptomic data.
- To provide a platform for systems biology and pharmacology approaches to develop novel ILD diagnostics and therapeutics.
Main Methods:
- Retrieved and curated 30 transcriptomics datasets (DNA microarrays, RNA-seq) from NCBI Gene Expression Omnibus and European Nucleotide Archive.
- Standardized data preprocessing, metadata curation, and quality control were applied to 1371 samples.
- Developed a robust data model for phenotypic data standardization to ensure cross-dataset comparability.
Main Results:
- Generated a comprehensive compendium of transcriptomics data for 1371 ILD and healthy samples.
- Provided gene expression data and lists of differentially expressed genes between ILD and healthy cohorts.
- Inferred co-expression networks for idiopathic pulmonary fibrosis (IPF), the most represented ILD, and healthy controls.
Conclusions:
- The curated compendium significantly improves the FAIRness of ILD transcriptomic data.
- This integrated resource supports systems biology and pharmacology research for ILD.
- Facilitates the development of novel diagnostic and therapeutic strategies for interstitial lung diseases.
