Integration of cytogenetic aberrations and in silico pathway enrichment identifies novel candidate genes in esophageal squamous cell carcinoma

Table 3 Prioritized candidate genes derived from recurrent cytobands and validated in The Cancer Genome Atlas esophageal squamous cell carcinoma cohort

Gene	Cytoband	Functional role	TCGA alteration type	TCGA frequency (%)	Supporting evidence
TP53	17p13	Linker gene/tumor suppressor	Mutation	84%	Established ESCC driver
STAT3	17q21	Linker gene/signaling	Amplification	4%	Copy-number gene-dosage (increase)
MAPK3	16p11	Pathway gene/MAPK signaling	Amplification	2%	Copy-number gene-dosage (increase)
WWOX	16q23	Tumor suppressor	Deep deletion	36%	Copy-number gene-dosage (reduce)
JUP	17q21	Linker gene/adhesion	Mutation/copy number alterations	10%	Network hub connectivity
AR	Xq12	Linker gene/hormone signaling	Amplification	4%	Hormonal pathway involvement
GATA2	3q21	Pathway gene/transcription	Low-frequency alteration	7%	Significant co-expression (ρ = 0.41)
MAL	2q11	Linker gene/tumor suppressor	Deletion (low frequency)	2%	Silenced in ESCC (literature)
GALNT3	2q24	Linker gene/glycosylation	Low-frequency alteration	2%	Network connectivity

The Cancer Genome Atlas dataset: Esophageal squamous cell carcinoma (Firehose Legacy), n-184 tumors. ESCC: Esophageal squamous cell carcinoma; TCGA: The Cancer Genome Atlas.