Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

Savola, Suvi; Klami, Arto; Tripathi, Abhishek; Niini, Tarja; Serra, Massimo; Picci, Piero; Kaski, Samuel; Zambelli, Diana; Scotlandi, Katia; Knuutila, Sakari

doi:10.1186/1471-2407-9-17

BMC Cancer

Table 3 Putative target genes for tumorigenesis and tumor progression in recurrent copy number changes of the 16 ESFT patients included in the integration analysis.

From: Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

Symbol	Name	Cytoband	Location¹	Correlation	p-value	Copy number status²	q-value	Functional information
HEATR3	HEAT repeat containing 3	16q12.1	48697286–48697733	0,876	2,2E-16	Deleted	6,05E-13	NA
TRAFD1	TRAF-type zinc finger domain containing 1	12q24.12	111075038–111075556	0,853	2,2E-16	Gained	6,05E-13	[47]
C1orf131	Chromosome 1 open reading frame 131	1q42.2	229426179–229426672	0,850	2,2E-16	Unspecified	6,05E-13	NA
HDGF	Hepatoma-derived growth factor	1q21-q23	154978607–154979115	0,844	1,5E-05	Gained	0,024182394	[34, 36–38]
DDX47	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	12p13.1	12873623– 12874134	0,844	1,5E-05	Gained	0,024182394	[48]
GIGYF2	GRB10 interacting GYF protein 2	2q37.1	233431003–233431539	0,838	3,5E-05	Unspecified	0,047741159	[49–51]
C2orf49	Chromosome 2 open reading frame 49	2q12.2	105331075–105331416	0,832	5,9E-05	Unspecified	0,069391132	NA
TMEM63A	Transmembrane protein 63A	1q42.12	224110806–224111244	0,829	7,3E-05	Gained	0,07491325	NA
WDR67	WD repeat domain 67	8q24.13	124233227–124233523	0,826	8,8E-05	Gained	0,080319015	NA
GSDMD1	Gasdermin D	8q24.3	144710202–144710602	-0,821	1,3E-04	Gained	0,107927089	NA
GPATCH2	G patch domain containing 2	1q41	215848737–215849264	0,812	1,8E-04	Unspecified	0,137376561	NA
WSB2	WD repeat and SOCS box-containing 2	12q24.23	116955326–116955682	0,809	2,1E-04	Unspecified	0,142275217	[42]
CACNA1C	Calcium channel, voltage-dependent, L type, alpha 1C subunit	12p13.3	2670999–2671234	-0,803	2,7E-04	Deleted	0,160672631	[40, 41]
KRT79	Keratin 79	12q13.13	51501640–51502010	-0,800	3,0E-04	Unspecified	0,160672631	NA
PPHLN1	Periphilin 1	12q12	41121456–41121979	0,797	3,2E-04	Gained	0,160672631	[43, 44]
C1orf107	Chromosome 1 open reading frame 107	1q32.2	208096981–208097464	0,794	3,5E-04	Gained	0,160672631	NA
FBXL14	F-box and leucine-rich repeat protein 14	12p13.33	1570852–1571348	0,794	3,5E-04	Unspecified	0,160672631	NA
ANKRD11	Ankyrin repeat domain 11	16q24.3	87999533–87999771	0,794	3,5E-04	Deleted	0,160672631	[45, 52]
HEATR1	HEAT repeat containing 1	1q43	234815741–234816376	0,791	3,9E-04	Gained	0,160672631	NA
COG2	Component of oligomeric golgi complex 2	1q42.2	228895774–228896323	0,791	3,9E-04	Gained	0,160672631	[39]

¹Location of the Affymetrix target sequence using BLAST algorithm. ²Copy number status = characterization of the copy number status in the whole patient set; unspecified indicates that both amplifications and deletions were found. NA = not available.

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ISSN: 1471-2407

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