ICBatlas

ICBatlas aggregates transcriptomic and clinical data from patients undergoing immune checkpoint blockade (ICB) therapy to enable comparative analyses of transcriptional mechanisms associated with treatment response across cancers.

Key Features:

• Data Integration: Consolidates transcriptome and clinical data from Gene Expression Omnibus, ArrayExpress, The Cancer Genome Atlas, and dbGaP encompassing 1,515 patient samples from 25 studies across nine cancer types.
• Sample Classification and Comparative Analyses: Classifies samples into response/nonresponse (R vs NR) or pretreatment/on-treatment (Pre vs On) groups and performs differential expression profiling, pathway enrichment assessments, and immune cell infiltration evaluations between groups.
• Response Score (RS): Implements a metric that quantifies the impact of gene expression on treatment response by integrating the variability degree and frequency of dysregulated genes in responders.
• Functional Insights: Reports associations among clinical outcomes, treatment-related genes, biological pathways, and immune cell infiltration patterns across cancer types and treatment stages.
• Stratified Transcriptomic Resolution: Represents transcriptomic features at dataset, cancer-type, and immune-checkpoint-specific levels and enables comparison of gene impact on response via the RS metric.

Scientific Applications:

• Mechanistic Studies: Elucidates transcriptional changes associated with ICB treatment and their implications for cancer biology.
• Biomarker Discovery: Identifies genes and pathways predictive of patient response to ICB therapy.
• Immunological Insights: Characterizes immune cell dynamics and infiltration patterns in the tumor microenvironment during ICB therapy.

Methodology:

Aggregates transcriptome and clinical data from GEO, ArrayExpress, TCGA, and dbGaP; classifies samples into R vs NR and Pre vs On groups; performs differential expression analysis, pathway enrichment studies, and immune cell infiltration assessments; and computes the Response Score by integrating the variability degree and frequency of dysregulated genes in responders.