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fusion(), fus()

fusion() or fus() expressions can be used in place of a namespace value within a gene, RNA, or protein abundance function to represent a hybrid gene, or gene product formed from two previously separate genes. fusion() expressions take the general form:

fus(ns5:v5, range5', ns3:v3, range3')

where ns5:v5 is a namespace and value for the 5' fusion partner, range5' is the sequence coordinates of the 5' partner, ns3:v3 is a namespace and value for the 3' partner, and range3' is the sequence coordinates for the 3' partner.

Example

RNA abundance of fusion with known breakpoints
r(fus(HGNC:TMPRSS2, r.1_79, HGNC:ERG, r.312_5034))

The r. designation in the range fields indicates that the numbering uses the RNA sequence as the reference. RNA sequence numbering starts at the transcription initiation site.

RNA abundance of fusion with unspecified breakpoints
r(fus(HGNC:TMPRSS2, ?, HGNC:ERG, ?))
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