Microenvironmental genomic alterations reveal signaling networks for head and neck squamous cell carcinoma

Table 3 Proteins in the signaling networks associated with structural hot- and cold-spots generated for stroma and epithelium of HNSCC

Category	Stroma	Epithelium
Tumor Suppressor Gene	ACVR1B, DOK2, PARK2, PTPN6, STAT5A	DOK2, PTPN6, STAT5A
Proto-oncogene	CRK, *EGFR* , LCK, SRC	*EGFR*, LCK, PARK2, SRC
HNC Biomarker	SFN	CAV3
Oncogenic when overexpressed	RHOA
Increased expression in Cancers	CDC2, CREM, HOXB4, NTSR2, PVR, PVRL1	ADRBK1, *CCR4* , HOXB4
Inactive in Cancers		DAB1
Serine/threonine protein kinase	CAMK2A, *GSK3A*	PRKCG
Role in Metastasis	GSC, PLCG1	PLCB1, PLCG1
HNSCC association not identified yet	ADAM15, BSN, CBLC, CNTN4, EMX1, GRIN2B, HOXB1, KRT82, SKAP1, TLE6	DSCAM, EMX1, GRIN2B, HOXB1, SKAP1, TLE6

The categories are determined by consensus literature terms. Genes whose products are studied as or utilized as drug targets are emboldened. Overall, 31 proteins in stroma and 21 for epithelium are identified through the signaling pathway search framework (Refer to Additional File 1 Table S6 and Table S7 for more details and references).