GIDISdb: a gene expression database for exploring human immune responses in infectious diseases

Area of Science:

• Infection Immunology
• Transcriptomics
• Bioinformatics

Background:

• Understanding human immune responses to infectious diseases requires transcriptomic analysis.
• Existing resources lack comprehensive integration of infectious disease transcriptomes and immune-focused analyses.
• A unified database is needed to facilitate cross-disease immune response studies.

Purpose of the Study:

• To develop GIDISdb (Gene expression database for Infectious DISeases), a novel resource integrating diverse infectious disease transcriptomic data.
• To provide an immune-centric analytical framework for cross-disease transcriptomic analysis.
• To enable detailed investigation of immune mechanisms and biomarker discovery in infectious diseases.

Main Methods:

• Integrated 3949 whole-blood RNA-seq samples from 51 projects covering 15 types of bacterial, viral, and fungal infections.
• Implemented standardized analytical workflows including differential expression and gene set enrichment analysis.
• Incorporated immune-specific annotations from ImmPort, Reactome, and Gene Ontology, alongside immune cell abundance estimation.

Main Results:

• GIDISdb facilitates comprehensive transcriptome analysis across various infectious diseases.
• Case study on tuberculosis revealed distinct immune profiles for latent (LTBI) and active (TB) forms.
• LTBI showed upregulated microbial defense and downregulated inflammatory genes, with altered immune cell populations compared to controls and active TB.

Conclusions:

• GIDISdb is a valuable, immune-centric platform for infection immunology research.
• The database accelerates the discovery of infection-specific immune mechanisms and biomarkers.
• GIDISdb provides a foundation for understanding complex host-pathogen interactions through transcriptomic data.