Prediction of chemo-response in serous ovarian cancer

Gonzalez Bosquet, Jesus; Newtson, Andreea M.; Chung, Rebecca K.; Thiel, Kristina W.; Ginader, Timothy; Goodheart, Michael J.; Leslie, Kimberly K.; Smith, Brian J.

doi:10.1186/s12943-016-0548-9

Molecular Cancer

Table 4 Genomic information and reason for inclusion in the original 422-gene signature for the 34 genes selected in the prediction model

From: Prediction of chemo-response in serous ovarian cancer

Annotation						Expression	Copy number		DNA Methylation		miRNA expression
Symbol	Name	Entrez-ID	chr	Start	Length	Fold-change (CR/IR)	Presence	cytoband	Methylated Genes	Methylation Status (CR/IR)	miRNA	CR/IR expression
LRRC8D	leucine rich repeat containing 8 family, member D	55144	1	90286572	115417	1.13
OLFML3	olfactomedin-like 3	56944	1	114522029	2846	0.76
DPT	dermatopontin	1805	1	168664694	33748	0.9
FAP	fibroblast activation protein, alpha	2191	2	163027199	72846	0.7
RNF13	ring finger protein 13	11342	3	149530474	149451		Gain	3q22.1-q29	CRKRS	1.19
SLC7A11	solute carrier family 7, (cationic amino acid transporter, y + system) member 11	23657	4	139085247	78256		Loss	4q13.3-q35.2
TRIO	triple functional domain (PTPRF interacting)	7204	5	14143828	365630	1.18	Gain	5p15.33-p13.1
DROSHA	drosha, ribonuclease type III	29102	5	31400601	131681	1.16	Gain	5p15.33-p13.1
RPS23	ribosomal protein S23	6228	5	81569138	5097	0.96	Loss	5q11.2-q21.1	UNQ9217	1.15	miR-22	0.8
SYNE1	spectrin repeat containing, nuclear envelope 1	23345	6	152442821	196658		Loss	6q15-q27	LAD1, NFATC2, SLC1A2, STEAP4	0.77	miR-22, miR-200b	1.22
STEAP4	STEAP family member 4	79689	7	87905743	30466				SYNE1	0.82
PRSS1	protease, serine, 1 (trypsin 1)	5644	7	142457318	3609	1.32	Gain	7q32.1-q36.3
PRSS2	protease, serine, 2 (trypsin 2)	5645	7	142479907	1471	1.34	Gain	7q32.1-q36.3
ST18	suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)	9705	8	53023391	299048	0.97	Gain	8p11.21-q24.3
RPS20	ribosomal protein S20	6224	8	56980738	6402		Gain	8p11.21-q24.3			miR-135b	1.22
ZBTB10	zinc finger and BTB domain containing 10	65986	8	81398447	36163	1.2	Gain	8p11.21-q24.3			miR-708	1.2
MTAP	methylthioadenosine phosphorylase	4507	9	21802634	63335	1.12	Loss	9p21.3-p21.2
GCNT1	glucosaminyl (N-acetyl) transferase 1, core 2	2650	9	79056581	65751	1.17
C10orf26	WBP1L - chromosome 10 open reading frame 26	54838	10	104503726	72295	0.87	No
MYO7A	myosin VIIA	4647	11	76839309	86977	1.08	Gain	11q13.5-q14.1
PDGFD	platelet derived growth factor D	80310	11	103777913	257114	0.76	No
KLRAP1	killer cell lectin-like receptor subfamily A pseudogene 1	10748	12	10741076	11358		Gain	12p13.33-p11.21			miR-22	0.8
NUAK1	NUAK family, SNF1-like kinase, 1	9891	12	106457124	76687	0.75	No
POLE	polymerase (DNA directed), epsilon	5426	12	133200347	63598	1.14	No
ENTPD5	ectonucleoside triphosphate diphosphohydrolase 5	957	14	74433180	52846	1.13	No
THBS1	thrombospondin 1	7057	15	39873279	16389		Loss	15q11.1-q21.1	CORO6, LAD1, NFATC2, SLC1A2, SNAI1	0.74	miR-22, miR-641, miR-200b	1.22
CCPG1	cell cycle progression 1	9236	15	55647437	53137	0.84	Loss	15q21.3
PDPR	pyruvate dehydrogenase phosphatase regulatory subunit	55066	16	70147528	47656	1.04	Loss	16q12.2-q24.3
RHOT1	ras homolog gene family, member T1	55288	17	30469472	83274	0.87	Gain	17p13.3-q21.2
MLX	MAX-like protein X	6945	17	40719077	6144	0.88	No
COPZ2	coatomer protein complex, subunit zeta 2	51226	17	46103532	11620	0.78	No
MATK	megakaryocyte-associated tyrosine kinase	4145	19	3777966	8449	0.93	No
TIMP3	TIMP metallopeptidase inhibitor 3	7078	22	33196801	62227	0.7	Loss	22q11.22			miR-22	0.8
MCM5	minichromosome maintenance complex component 5	4174	22	35796115	24380	1.19	Loss	22q11.22-q13.33

In the Expression, Copy number, DNA methylation, and miRNA expression, only those with significant differential values between CR and IR were represented. Some genes had more than one biological difference
Copy number shows the chromosomal region (cytoband) that was significantly correlated with gene expression in the 422-gene signature. DNA Methylation and miRNA expression shows the initial variables that were significantly correlated to gene expression in the 422-gene signature

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ISSN: 1476-4598

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