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Functional Annotation of the Mammalian Genome (FANTOM)

Definition
AI-generated

FANTOM (Functional Annotation of the Mammalian Genome) is a series of international projects that profile gene expression and regulation at scale—especially using CAGE to map transcription start sites, promoters, and enhancer activity across cell types and tissues—producing widely used atlases and annotations.

Topics
Cohorts and databases
Synonyms
FANTOM
Related
Cap Analysis of Gene Expression (CAGE-seq) Encyclopedia of DNA Elements (ENCODE) Genome Annotation

Why it matters in GWAS

FANTOM-based promoter and enhancer maps help place noncoding GWAS variants relative to active transcription initiation and regulatory elements in relevant lineages, supporting mechanistic interpretation with expression and chromatin data. Where association signals fall near or within lncRNAs, FANTOM6-style interactome-backed annotation can narrow plausible mechanisms (e.g. altered RBP occupancy or RNA-mediated regulation) alongside coding and enhancer-centric views.

Example usage

"We checked whether the credible-set SNPs overlapped FANTOM-defined enhancers in primary monocytes."

Cap Analysis of Gene Expression (CAGE-seq) Encyclopedia of DNA Elements (ENCODE) Genome Annotation Long non-coding RNA (lncRNA) Transcription Start Site (TSS)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Carninci P, et al. (2005). The transcriptional landscape of the mammalian genome. Science.
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