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Cap Analysis of Gene Expression (CAGE-seq)

Definition
AI-generated

CAGE (cap analysis of gene expression) maps the 5′ ends of capped RNAs genome-wide, usually by short-tag sequencing, to infer transcription start sites (TSSs) and promoter usage.

Topics
Sequencing and omics tech
Synonyms
CAGE CAGE seq
Related
No-amplification non-tagging CAGE (nAnT-iCAGE) Functional Annotation of the Mammalian Genome (FANTOM) ChIP-seq (Chromatin Immunoprecipitation Sequencing)

Why it matters in GWAS

Noncoding associations near promoters may depend on which TSS isoform is active in a tissue; CAGE-informed annotation clarifies whether a variant sits in a core promoter or an alternative TSS peak. It supports interpretation alongside chromatin accessibility and eQTL data.

Example usage

"CAGE-seq peaks highlighted alternative transcription start sites near the associated gene."

No-amplification non-tagging CAGE (nAnT-iCAGE) Functional Annotation of the Mammalian Genome (FANTOM) ChIP-seq (Chromatin Immunoprecipitation Sequencing) Encyclopedia of DNA Elements (ENCODE) Genome Annotation Read tag RNA Sequencing (RNA-seq)
Related-term network

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References

  • Shiraki T, et al. (2003). Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA.
  • Ji HJ, Pertea M, Salzberg SL. (2026). Annotating genomes at increased scale and resolution. Nat Rev Genet. https://doi.org/10.1038/s41576-026-00937-3
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