Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu)

Luan, Jinwei; Li, Xianglan; Guo, Rutao; Liu, Shanshan; Luo, Hongyu; You, Qingshan

doi:10.1515/raon-2016-0010

Figures & Tables

Venn diagram of DEGs between 0 GY X-ray-treated FaDu cells and 8 GY X-ray-treated FaDu cells, as well as the DEGs between 8 GY X-ray-treated FaDu cells and 8 GY X-ray + RITA-treated FaDu cells.

The PPI network for the RITA genes and their related DEGs. The red hubs represent the up-regulated DEGs; the green hubs represent the down-regulated DEGs; the triangle hubs represent the RITA genes; the lines represent the interactions between the genes.

Functional annotation for RFC2 and EZH2 clusters. Node color represents the functional groups; node size reflects the p-value, with the smaller the node size indicating larger p-values, while the larger node size represents smaller p-values.

The KEGG pathway enrichment for the DEGs between 0 GY X-ray treated FaDu cells and 8 GY X-ray treated FaDu cells, as well as 8 GY X-ray treated FaDu cells and 8 GY X-ray + RITA treated FaDu cells_

Term	Count	P value	Gene symbols
gy8ctl vs. gy0ctl
hsa03030: DNA replication	28	5.85E-19	POLA1, POLA2, RPA3, RPA1, PRIM1, RPA2, POLE4, MCM7, POLE3, FEN1
hsa04110: Cell cycle	43	1.91E-11	E2F1, E2F2, DBF4, PRKDC, PKMYT1, CHEK1, CDC45, MCM7, CDKN2B, CDKN2C …
hsa03430: Mismatch repair	16	1.15E-09	EXO1, SSBP1, MSH2, LIG1, MLH1, RPA3, RFC5, POLD3, RPA1, RPA2 …
hsa00240: Pyrimidine metabolism	32	2.00E-08	POLR2G, DTYMK, POLA1, CAD, POLA2, CMPK2, TK1, PRIM1, TYMS, POLE4 …
hsa03410: Base excision repair	16	2.06E-06	HMGB1, UNG, NEIL3, LIG1, POLE, NEIL1, POLD3, POLD4, POLE4, POLE3 …
hsa03440: Homologous recombination	14	3.36E-06	RAD51C, XRCC3, NBN, BLM, SSBP1, MRE11A, EME1, RPA3, RAD51, POLD3 …
hsa03420: Nucleotide excision repair	15	2.25E-04	LIG1, POLE, RPA3, RFC5, POLD3, RPA1, RPA2, POLD4, RFC3, POLE4 …
hsa00230: Purine metabolism	33	3.73E-04	XDH, POLR2G, POLA1, POLA2, PFAS, PRIM1, POLE4, POLE3, PDE4A, ENTPD8 …
hsa05200: Pathways in cancer	52	0.010417112	FGF19, E2F1, HSP90AB1, E2F2, PTGS2, PDGFB, PGF, STAT5A, ARNT2, FGF11 …
hsa05219: Bladder cancer	11	0.016627297	E2F1, E2F2, TYMP, CDKN1A, PGF, VEGFA, RB1, DAPK2, CDK4, MMP2, DAPK1
hsa04115: p53 signaling pathway	15	0.018499656	CDK1, CYCS, CHEK1, ATR, CDK4, CCNG2, GTSE1, CCNB1, CDKN1A, CCNB2 …
hsa04512: ECM-receptor interaction	17	0.024887625	HSPG2, SDC4, COL5A1, CHAD, HMMR, VWF, LAMB3, LAMB2, ITGB8, ITGA5 …
hsa03020: RNA polymerase	8	0.03298698	POLR3G, POLR2G, POLR3K, POLR1E, POLR1A, POLR1C, POLR1B, POLR3B
hsa00970: Aminoacyl-tRNA biosynthesis	10	0.036943456	IARS, NARS2, LARS, FARSB, EPRS, WARS2, DARS2, AARS2, KARS, EARS2
hsa03040: Spliceosome	22	0.044130211	NCBP1, MAGOH, TRA2B, LSM6, TRA2A, SNRPD1, HSPA1A, PRPF4, RBMX, HNRNPA1 …
hsa05222: Small cell lung cancer	16	0.048720159	E2F1, TRAF1, E2F2, CKS1B, PTGS2, PIK3CD, CYCS, SKP2, RB1, BIRC3 …
gy8rita vs. gy8ctl
hsa03410: Base excision repair	4	0.014381142	NEIL1, LIG3, PARP3, SMUG1
hsa05212: Pancreatic cancer	5	0.021107952	AKT1, PGF, PIK3CB, ERBB2, RALGDS
hsa05213: Endometrial cancer	4	0.040674333	AKT1, PIK3CB, ERBB2, CTNNA1
hsa04150: mTOR signaling pathway	4	0.040674333	AKT1, PGF, PIK3CB, EIF4E2

The top ten up- and down-regulated DEGs between 0 GY X-ray treated FaDu cells and 8 GY X-ray treated FaDu cells, as well as 8 GY X-ray treated FaDu cells and 8 GY X-ray + RITA treated FaDu cells_

	Gene symbols	log2 fold change	P-value	Gene symbols	log2 fold change	P-value
	BMF	−1.79769e+308	1.23E-11	BMF	−1.79769e+308	1.23E-11
	SDCBP	−1.79769e+308	0.00097112	SDCBP	−1.79769e+308	0.00097112
	IL32	−1.79769e+308	0.0110064	IL32	−1.79769e+308	0.0110064
	MAD1L1	−1.79769e+308	9.77E-05	MAD1L1	−1.79769e+308	9.77E-05
	SIRT3	−1.79769e+308	0.00289562	SIRT3	−1.79769e+308	0.00289562
Up-regulated	KAZN	−1.79769e+308	7.93E-10	KAZN	−1.79769e+308	7.93E-10
	TSPAN4	−1.79769e+308	0.0136997	TSPAN4	−1.79769e+308	0.0136997
	PPAN-P2RY11	−1.79769e+308	4.71E-08	PPAN-P2RY11	−1.79769e+308	4.71E-08
	CDC14B	−1.79769e+308	1.49E-06	CDC14B	−1.79769e+308	1.49E-06
	CXCL16	−1.79769e+308	0.000434357	CXCL16	−1.79769e+308	0.000434357
	C3orf14	−5.88442	0.006353	KCTD2	−3.8901	1.23E-06
	TTC28-AS1	−3.10554	1.30E-09	TSPAN4	−3.68234	0.0124825
	KRT4	−2.86398	0	FGFR3	−3.47603	0.0322468
	ALPP	−2.68741	1.30E-13	PLEKHM1.1	−3.41618	0.0191408
	MND1	−2.64752	0.022297	CHFR	−3.39824	0.0369514
Down-regulated	DHRS2	−2.38983	4.17E-11	KREMEN2	−3.32824	0.033903
	FGF3	−2.33156	2.25E-12	SMAP2	−3.3199	0.0215792
	TERC	−2.268	0.027132	EPS15L1	−3.30518	0.00562372
	UTP20	−2.23728	0	MORF4L2	−3.0731	0.0300806
	GAL	−2.22661	0	PIGQ	−2.94079	0.0327601

SUMMARY statistics of paired-end (PE) RNA-Seq reads in six cell lines

Sample	Total PE reads	Total high quality PE reads	Total mapped PE reads	Total uniquely mapped PE reads
Sample_L141211001	10467886	8650424 (82.3%)	6846290 (79.1%)	6749179
Sample_L141211002	11510210	9627883 (83.6%)	7197526 (74.7%)	7097908
Sample_L141211003	11119410	9365349 (84.2%)	6910499 (73.7%)	6825529
Sample_L141211004	11271934	9510517 (84.3%)	6752339 (70.9%)	6669811
Sample_L141211005	10854414	9110446 (83.9%)	7129465 (78.2%)	7043831
Sample_L141211006	10532245	8802840 (83.5%)	6752224 (76.7%)	6671073

Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu)

Figures & Tables

The KEGG pathway enrichment for the DEGs between 0 GY X-ray treated FaDu cells and 8 GY X-ray treated FaDu cells, as well as 8 GY X-ray treated FaDu cells and 8 GY X-ray + RITA treated FaDu cells_

The top ten up- and down-regulated DEGs between 0 GY X-ray treated FaDu cells and 8 GY X-ray treated FaDu cells, as well as 8 GY X-ray treated FaDu cells and 8 GY X-ray + RITA treated FaDu cells_

SUMMARY statistics of paired-end (PE) RNA-Seq reads in six cell lines

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