Survival marker genes of colorectal cancer derived from consistent transcriptomic profiling

Martinez-Romero, Jorge; Bueno-Fortes, Santiago; Martín-Merino, Manuel; Ramirez de Molina, Ana; De Las Rivas, Javier

doi:10.1186/s12864-018-5193-9

BMC Genomics

Table 3 Genes selected as top-50 best survival markers of colorectal cancer (CRC)

From: Survival marker genes of colorectal cancer derived from consistent transcriptomic profiling

Number	GENE ENSEMBL_ID	GENE Symbol	KM.p.value (all-dt)	HR (all-dt)	N-signf-in-100i (KM.p.value)	HR (mean-in-100i)	GENE HGNC_ID	GENE DESCRIPTION
1	ENSG00000057019	DCBLD2	0.0000000000	2.02	99	2.106	24627	discoidin; CUB and LCCL domain containing 2 [HGNC:24627]
2	ENSG00000152104	PTPN14	0.0000000000	1.99	99	2.082	9647	protein tyrosine phosphatase; non-receptor type 14
3	ENSG00000125869	LAMP5	0.0000000000	1.99	93	2.046	16097	lysosomal associated membrane prot.member 5 [HGNC:16097]
4	ENSG00000169908	TM4SF1	0.0000000001	1.96	93	2.031	11853	transmembrane 4 L six family member 1 [HGNC:11853]
5	ENSG00000113389	NPR3	0.0000000002	1.95	97	2.136	7945	natriuretic peptide receptor 3 [HGNC:7945]
6	ENSG00000186007	LEMD1	0.0000000003	1.95	85	1.937	18,725	LEM domain containing 1 [HGNC:18725]
7	ENSG00000135338	LCA5	0.0000000003	1.89	97	2.021	31,923	LCA5; lebercilin [HGNC:31923]
8	ENSG00000169826	CSGALNACT2	0.0000000008	1.91	92	1.974	24,292	chondroitin sulfate N-acetylgalactosaminyltransferase 2
9	ENSG00000059804	SLC2A3	0.0000000014	1.93	89	1.993	11,007	solute carrier family 2 member 3 [HGNC:11007]
10	ENSG00000099860	GADD45B	0.0000000018	1.92	97	2.074	4096	growth arrest and DNA damage inducible beta [HGNC:4096]
11	ENSG00000136155	SCEL	0.0000000018	1.88	87	1.928	10,573	sciellin [HGNC:10573]
12	ENSG00000100625	SIX4	0.0000000019	1.89	91	1.951	10,890	SIX homeobox 4 [HGNC:10890]
13	ENSG00000131016	AKAP12	0.0000000028	1.85	95	2.092	370	A-kinase anchoring protein 12 [HGNC:370]
14	ENSG00000158270	COLEC12	0.0000000028	1.84	92	1.941	16,016	collectin subfamily member 12 [HGNC:16016]
15	ENSG00000154553	PDLIM3	0.0000000047	1.84	91	1.985	20,767	PDZ and LIM domain 3 [HGNC:20767]
16	ENSG00000082781	ITGB5	0.0000000049	1.82	88	1.911	6160	integrin subunit beta 5 [HGNC:6160]
17	ENSG00000144366	GULP1	0.0000000050	1.81	88	1.911	18,649	engulfment adaptor PTB domain containing 1 [HGNC:18649]
18	ENSG00000171951	SCG2	0.0000000051	1.81	93	2.034	10,575	secretogranin II [HGNC:10575]
19	ENSG00000185567	AHNAK2	0.0000000066	1.80	87	1.896	20,125	AHNAK nucleoprotein 2 [HGNC:20125]
20	ENSG00000138061	CYP1B1	0.0000000075	1.84	85	1.884	2597	cytochrome P450 family 1 subfamily B member 1 [HGNC:2597]
21	ENSG00000184304	PRKD1	0.0000000451	1.74	87	1.872	9407	protein kinase D1 [HGNC:9407]
22	ENSG00000152583	SPARCL1	0.0000000471	1.74	85	1.863	11,220	SPARC like 1 [HGNC:11220]
23	ENSG00000147883	CDKN2B	0.0000000717	1.73	84	1.847	1788	cyclin dependent kinase inhibitor 2B [HGNC:1788]
24	ENSG00000213190	MLLT11	0.0000001989	1.70	84	1.813	16,997	myeloid/lymphoid or mixed-lineage leukemia; translocated to 11
25	ENSG00000135218	CD36	0.0000002751	1.69	85	1.891	1663	CD36 molecule [HGNC:1663]
1	ENSG00000133216	EPHB2	0.0000000000	0.43	100	0.426	3393	EPH receptor B2 [HGNC:3393]
2	ENSG00000169718	DUS1L	0.0000000000	0.49	98	0.481	30,086	dihydrouridine synthase 1 like [HGNC:30086]
3	ENSG00000163545	NUAK2	0.0000000001	0.51	96	0.495	29,558	NUAK family kinase 2 [HGNC:29558]
4	ENSG00000158169	FANCC	0.0000000002	0.51	95	0.498	3584	Fanconi anemia complementation group C [HGNC:3584]
5	ENSG00000277972	CISD3	0.0000000002	0.51	87	0.511	27,578	CDGSH iron sulfur domain 3 [HGNC:27578]
6	ENSG00000099800	TIMM13	0.0000000003	0.53	95	0.511	11,816	translocase of inner mitochondrial membrane 13 [HGNC:11816]
7	ENSG00000116771	AGMAT	0.0000000005	0.52	95	0.515	18,407	agmatinase [HGNC:18407]
8	ENSG00000118513	MYB	0.0000000006	0.52	93	0.508	7545	MYB proto-oncogene. Transcription factor [HGNC:7545]
9	ENSG00000016391	CHDH	0.0000000006	0.53	90	0.520	24,288	choline dehydrogenase [HGNC:24288]
10	ENSG00000137460	FHDC1	0.0000000008	0.52	96	0.505	29,363	FH2 domain containing 1 [HGNC:29363]
11	ENSG00000132846	ZBED3	0.0000000009	0.52	88	0.522	20,711	zinc finger BED-type containing 3 [HGNC:20711]
12	ENSG00000162408	NOL9	0.0000000015	0.54	92	0.527	26,265	nucleolar protein 9 [HGNC:26265]
13	ENSG00000109534	GAR1	0.0000000017	0.50	99	0.479	14,264	GAR1 ribonucleoprotein [HGNC:14264]
14	ENSG00000133477	FAM83F	0.0000000019	0.54	93	0.518	25,148	family with sequence similarity 83 member F [HGNC:25148]
15	ENSG00000100348	TXN2	0.0000000036	0.53	88	0.527	17,772	thioredoxin 2 [HGNC:17772]
16	ENSG00000108479	GALK1	0.0000000036	0.55	88	0.525	4118	galactokinase 1 [HGNC:4118]
17	ENSG00000110917	MLEC	0.0000000045	0.55	96	0.476	28,973	malectin [HGNC:28973]
18	ENSG00000114738	MAPKAPK3	0.0000000048	0.55	92	0.520	6888	mitogen-activated protein kinase-activated 3 [HGNC:6888]
19	ENSG00000137752	CASP1	0.0000000180	0.56	87	0.523	1499	caspase 1 [HGNC:1499]
20	ENSG00000131844	MCCC2	0.0000000183	0.57	93	0.516	6937	methylcrotonoyl-CoA carboxylase 2 [HGNC:6937]
21	ENSG00000178409	BEND3	0.0000000193	0.55	88	0.529	23,040	BEN domain containing 3 [HGNC:23040]
22	ENSG00000114737	CISH	0.0000000216	0.55	87	0.508	1984	cytokine inducible SH2 containing protein [HGNC:1984]
23	ENSG00000011376	LARS2	0.0000000239	0.55	91	0.528	17,095	leucyl-tRNA synthetase 2; mitochondrial [HGNC:17095]
24	ENSG00000164045	CDC25A	0.0000000481	0.57	90	0.539	1725	cell division cycle 25A [HGNC:1725]
25	ENSG00000154655	L3MBTL4	0.0000000606	0.54	90	0.506	26,677	l(3)mbt-like 4 (Drosophila) [HGNC:26677]

The first part of the table corresponds to the top-25 genes where up-regulation corresponds to shorter survival and higher risk (i.e., HR > 1); the second part of the table corresponds to the top-25 genes where UP-regulation corresponds to longer survival and lower risk (HR < 1). The genes were ranked by their KM adjusted p values and the Hazard Ratio values calculated for the whole dataset, i.e. for all the 1273 samples (all-dt). The stability and robustness of the gene survival markers was assessed by cross-validation, applying to each gene a resampling strategy with random selection of 80% of the samples 100 times (i.e. doing 100 iterations). For the ranking we also considered that the genes had to give a significant adjusted p-value in more than 80 iterations (N-sinf-in-100i > 80)

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ISSN: 1471-2164

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