Transcriptomics 101 (cancer)
Transcriptomics measures RNA abundance and isoform usage. In tumors it reveals pathway activity, immune infiltration, and drug-response signatures.
Bulk RNA-seq
- Count matrix: genes × samples after alignment and quantification
- DE analysis: tumor vs normal, treatment arms, molecular subtypes
- Gene signatures: proliferation, hypoxia, immune scores — often used in trials and biomarker work
Single-cell and spatial
For heterogeneity and microanatomy, see Intro to single-cell and spatial.
Clinical angles
- Fusion transcripts (some assays are DNA; some are RNA-first)
- Immune repertoire and checkpoint-related expression patterns
- Companion diagnostics sometimes use expression (see Biomarkers)