SCAPER

Across TCGA pan-cancer cohorts, SCAPER mass-spec protein differs between tumor and matched normal tissue in 3 of 18 cancer types tested, making tumor–normal expression one of SCAPER’s most consistent transcriptional readouts.

The strongest signal is observed in head and neck squamous cell carcinoma (HNSC), where SCAPER mass-spec protein is repressed in tumor relative to normal tissue. In most cancer types SCAPER is over-expressed in tumor, although a few such as HNSC and PDAC show the opposite, repressed pattern.

HNSC, PDAC, and CCRCC are the cancer types where SCAPER tumor–normal differential expression is most reproducible.

mass-spec protein tumor vs normal associations by lineage

Ranked by sampling consensus. Fold-change is the tumor-versus-normal difference in SCAPER mass-spec protein (log₂); positive values indicate higher expression in tumor. p-values are from the differential-expression test.

Lineage	Gender	Stage	Fold-change	p	Sampling consensus
HNSC	Male	All	−0.282	<.001	6	view →
PDAC	All	All	−0.267	.001	4	view →
CCRCC	Male	All	+0.102	.015	2	view →

Pink = over-expressed in tumor, green = repressed in tumor. Showing the 3 strongest of 3 lineages.

SCAPER–HNSC

Open the HNSC breakdown →