LNCaP Atlas: Gene expression associated with in vivoprogression to castration-recurrent prostate cancer

Romanuik, Tammy L; Wang, Gang; Morozova, Olena; Delaney, Allen; Marra, Marco A; Sadar, Marianne D

doi:10.1186/1755-8794-3-43

BMC Medical Genomics

Table 4 Gene expression trends of LongSAGE tags that consistently and significantly altered expression in CR prostate cancer*

From: LNCaP Atlas: Gene expression associated with in vivoprogression to castration-recurrent prostate cancer

	13N			15N			13R
	AS§	RADII	CR¶	AS	RAD	CR	AS	RAD	CR
Tag Sequence	S1885	S1886	S1887	S1888	S1889	S1890	S1891	S1892	S1893	Trend‡	Gene**	Accession§§
TCTAGAGAACACTGTGC	12†	79	382	7	67	136	7	52	200	A	ACPP‡‡	NM_001099
TAATTTTTCTAAGGTGT	101	311	648	119	397	895	120	546	918	A	C1ORF80	ENSG00000186063
TGAGAGAGGCCAGAACA	8	39	150	4	39	144	7	33	95	A	N/A	Genomic
CTCATAAGGAAAGGTTA	637	952	1680	653	1170	1540	688	1620	1930	A	RNF208	BC090061
GATTTCTATTTGTTTTT	89	169	446	116	208	339	86	311	555	A	SERINC5	ENSG00000164300
GTTGGGAAGACGTCACC	426	571	742	273	417	741	262	363	495	A	STEAP1	NM_012449
GAGGATCACTTGAGGCC	191	299	449	134	189	589	187	203	314	B	AMACR‡‡	BC009471
TTGTTGATTGAAAATTT	219	197	528	273	197	479	232	391	586	B	AMD1‡‡	NM_001634
TTTGCTTTTGTTTTGTT	53	16	169	34	51	129	7	28	72	B	AQP3	NM_004925
GTTCGACTGCCCACCAG	45	28	101	52	47	122	34	42	106	B	ASAH1††	NM_177924
TAATAAACAGGTTTTTA	426	232	648	332	315	700	138	250	491	B	ASAH1‡‡	NM_177924
TCACAGCTGTGAAGATC	85	110	277	161	71	258	310	438	945	B	BTG1	NM_001731
AAAAGAGAAAGCACTTT	24	75	199	19	35	85	15	90	552	B	CAMK2N1	NM_018584
CAAAACAGGCAGCTGGT	4	71	169	15	83	162	37	75	268	B	CAMK2N1††	NM_018584
AGGAGGAAGAATGGACT	33	59	187	49	67	247	26	42	223	B	CCNH	NM_001239
TTTTAAAAATATAAAAT	89	83	243	97	130	269	64	170	382	B	COMT	NM_000754
GAATGAAATAAAAAATA	134	252	626	209	240	357	116	160	272	B	DHRS7	NM_016029
AAAGTGCATCCTTTCCC	118	146	318	153	220	394	288	231	646	B	FGFRL1	NM_001004356
AAACTGAATAAGGAGAA	24	51	236	19	51	438	19	146	283	B	GALNT3	NM_004482
TTTAAGGAAACATTTGA	4	4	75	4	4	81	0	0	57	B	GALNT3††	NM_004482
CCAACCGTGCTTGTACT	191	327	521	202	279	534	172	363	510	B	GLO1	NM_006708
GAGGGCCGGTGACATCT	300	378	1170	321	476	1230	254	447	1030	B	H2AFJ	NM_177925
TATCATTATTTTTACAA	57	63	161	67	63	181	75	94	181	B	HSD17B4	NM_000414
AATGCACTTATGTTTGC	16	8	64	22	16	77	19	28	98	B	N/A	No map
ACCTTCGCAGGGGAGAG	0	0	19	0	4	41	0	5	34	B	N/A	Genomic
ATAACCTGAAAGGAAAG	0	16	56	7	4	74	0	28	87	B	N/A	No map
GTGATGTGCACCTGTTG	0	0	38	4	0	30	0	5	45	B	N/A	No map
GTTTGGAGGTACTAAAG	20	43	94	34	87	169	34	90	234	B	N/A	Genomic
TTTTCAAAAATTGGAAA	0	35	180	7	4	59	0	19	61	B	N/A	No map
GAAAAATTTAAAGCTAA	394	397	569	433	598	788	853	862	1060	B	NGFRAP1	NM_206917
CAAATTCAGGGAGCACA	0	4	139	4	16	228	0	14	136	B	OPRK1	NM_000912
CTATTGTCTGAACTTGA	0	8	109	0	12	70	0	9	227	B	OR51E2	BC020768
ATGCTAATTATGGCAAT	4	12	75	4	8	74	0	5	57	B	PCGEM1	NR_002769
CAGAAAGCATCCCTCAC	4	43	195	0	16	111	7	33	264	B	PLA2G2A‡‡	NM_000300
TAATTTTAGTGCTTTGA	16	75	154	37	59	162	4	57	132	B	PTGFR	NM_000959
TTGTTTGTAAATAGAAT	0	12	94	0	4	162	0	14	72	B	QKI	NM_206853
TAAACACTGTAAAATCC	0	4	75	0	4	66	0	0	42	B	QKI††	NM_206853
AGCAGATCAGGACACTT	20	35	112	15	16	140	15	42	98	B	S100A10	NM_002966
CTGCCATAACTTAGATT	37	55	161	93	63	192	56	99	264	B	SBDS	NM_016038
TGGCTGAGTTTATTTTT	20	24	79	41	8	96	4	42	147	B	SFRS2B	NM_032102
GAAGATTAATGAGGGAA	126	142	277	108	130	402	101	188	325	B	SNX3	NM_003795
ATGGTACTAAATGTTTT	16	47	124	37	28	88	11	19	76	B	SPIRE1	NM_020148
TATATATTAAGTAGCCG	45	39	101	45	75	133	41	75	178	B	STEAP2‡‡	NM_152999
CAACAATATATGCTTTA	24	32	82	75	32	136	26	99	212	B	STEAP2††	NM_152999
TTTCATTGCCTGAATAA	24	43	150	34	59	114	22	61	178	B	TACC1‡‡	NM_006283
TTGGCCAGTCTGCTTTC	8	16	67	4	4	77	0	5	38	B	TMEM30A	ENSG00000112697
ATATCACTTCTTCTAGA	12	4	26	7	4	26	0	52	140	C	ADAM2‡‡	NM_001464
ATGTGTGTTGTATTTTA	812	338	768	1010	315	1020	269	702	865	C	BNIP3	NM_004052
CCACGTTCCACAGTTGC	601	291	599	530	346	700	381	339	559	C	ENO2	NM_001975
CTGATCTGTGTTTCCTC	16	0	26	0	4	41	19	0	34	C	HLA-B	BC013187
AGCCCTACAAACAACTA	382	441	596	508	456	619	400	631	1010	C	MT-ND3	ENSG00000198840
ATATTTTCTTTGTGGAA	20	12	90	7	0	48	4	0	23	C	N/A	No map
CAAGCATCCCCGTTCCA	2400	2130	2440	2730	1720	2250	1020	2010	2340	C	N/A	ENSG00000211459
GTTGTAAAATAAACTTT	118	83	172	228	87	247	112	203	378	C	N/A	Genoic
TTGGATTTCCAAAGCAG	12	0	19	0	0	33	0	0	26	C	N/A	Genomic
TCTTTTAGCCAATTCAG	138	181	420	381	326	468	389	334	457	C	NKX3-1††	NM_006167
TGATTGCCCTTTCATAT	73	39	86	86	39	107	108	99	181	C	P4HA1	NM_000917
GTAACAAGCTCTGGTAT	28	16	56	49	24	66	11	19	72	C	PJA2	NM_014819
ACAGTGCTTGCATCCTA	85	75	139	108	98	203	101	118	196	C	PPP2CB	NM_004156
AGGCGAGATCAATCCCT	57	39	101	37	24	122	131	66	268	C	PSMA7	NM_002792
TATTTTGTATTTATTTT	73	59	180	93	51	111	22	94	253	C	SLC25A4	NM_001151
TTATGGATCTCTCTGCG	1050	1260	1820	1140	1300	2260	1990	1010	1530	C	SPON2	NM_012445
CAGTTCTCTGTGAAATC	767	515	1060	855	503	914	467	608	1200	C	TMEM66	NM_016127
AAATAAATAATGGAGGA	138	59	255	82	118	284	165	90	159	C	TRPM8	NM_024080
ATGTTTAATTTTGCACA	61	87	154	157	59	195	217	85	344	C	WDR45L	NM_019613
GGGCCCCAAAGCACTGC	861	543	1180	1020	657	1590	1240	739	937	E	C19orf48	NM_199249
TCCCCGTGGCTGTGGGG	1670	1390	2290	1740	1410	1720	3370	970	1180	E	DHCR24‡‡	BC004375
GCATCTGTTTACATTTA	487	201	345	444	208	468	684	226	423	E	ELOVL5	NM_021814
GAAATTAGGGAAGCCTT	317	153	311	310	181	542	359	193	298	E	ENDOD1	XM_290546
GGATGGGGATGAAGTAA	2780	1160	4780	2950	1350	3620	2930	1230	1890	E	KLK3‡‡	NM_001648
TGAAAAGCTTAATAAAT	313	142	322	474	181	332	273	179	314	E	TPD52	NM_001025252
GTTGTGGTTAATCTGGT	1770	634	1270	1800	806	1190	2480	659	960	F	B2M	NM_004048
GAAACAAGATGAAATTC	4380	1170	2260	5300	1110	2720	3750	2220	2830	F	PGK1	NM_000291
AGCACCTCCAGCTGTAC	2150	1130	648	2060	1560	939	1560	1200	722	G	EEF2	NM_001961
GCACAAGAAGATTAAAA	536	228	124	762	425	195	838	278	174	G	GAS5	NR_002578
CCGCTGCGTGAGGGCAG	451	169	56	429	197	44	516	94	0	G	HES6	NM_018645
GCCCAGGTCACCCACCC	585	55	4	519	79	7	456	66	0	G	LOC644844	XM_927939
ATGCAGCCATATGGAAG	2650	386	82	2470	216	129	1210	259	98	G	ODC1	NM_002539
CGCTGGTTCCAGCAGAA	1420	811	479	1250	959	553	800	589	374	G	RPL11	NM_000975
AAGACAGTGGCTGGCGG	2650	1730	1220	2460	1860	1350	2120	1630	1270	G	RPL37A‡‡	NM_000998
TTCTTGTGGCGCTTCTC	925	543	217	1030	708	273	1130	419	306	G	RPS11††	NM_001015
GGTGAGACACTCCAGTA	463	252	165	485	346	192	363	245	159	G	SLC25A6	NM_001636
AGGTTTTGCCTCATTCC	982	515	281	1200	491	243	688	782	166	H	ABHD2	NM_007011
TGAAGGAGCCGTCTCCA	317	272	187	392	295	199	366	259	140	H	ATP5G2	NM_001002031
CTCAGCAGATCCAAGAG	191	185	67	254	232	66	142	231	79	H	C17orf45	NM_152350
CTGTGACACAGCTTGCC	308	397	172	209	307	125	295	226	110	H	CCT2	NM_006431
TCTGCACCTCCGCTTGC	495	606	277	426	570	276	366	471	204	H	EEF1A2	NM_001958
GCCCAAGGACCCCCTGC	114	114	38	138	98	41	101	42	4	H	FLNA‡‡	NM_001456
TTATGGGATCTCAACGA	564	425	180	642	452	317	430	490	253	H	GNB2L1	NM_006098
TCTGCAAAGGAGAAGTC	81	102	38	105	87	26	165	80	30	H	HMGB2	NM_002129
CTTGTGAACTGCACAAC	268	228	124	231	177	103	273	160	57	H	HN1	NM_016185
TCTGAAGTTTGCCCCAG	313	291	150	254	299	155	187	226	72	H	MAOA	NM_000240
TTAATTGATAGAATAAA	483	350	199	422	287	103	273	235	83	H	MAOA	NM_000240
GGCAGCCAGAGCTCCAA	1200	1260	420	1050	672	350	681	819	23	H	MARCKSL1	NM_023009
CCCTGCCTTGTCCCTCT	353	240	112	310	263	107	176	193	102	H	MDK	NM_001012334
CTGTGGATGTGTCCCCC	649	476	169	459	389	214	430	297	117	H	N/A	No map
CTCCTCACCTGTATTTT	1120	771	262	1220	979	313	666	730	261	H	RPL13A‡‡	NM_012423
GCAGCCATCCGCAGGGC	1980	1770	809	2300	1730	928	2150	1570	1020	H	RPL28	NM_000991
GGATTTGGCCTTTTTGA	3470	2070	1370	4170	2910	1540	2800	2870	2500	H	RPLP2‡‡	NM_001004
TCTGTACACCTGTCCCC	2320	1670	850	1930	1880	825	2130	1490	1120	H	RPS11	NM_001015
GCTTTTAAGGATACCGG	1510	1050	626	1860	1120	593	1550	1550	960	H	RPS20‡‡	NM_001023
CCCCAGCCAGTCCCCAC	921	519	281	788	664	357	1100	438	291	H	RPS3	NM_001005
CCCCCAATGCTGAGGCC	89	138	26	90	94	30	90	80	30	H	SF3A2	NM_007165
GCCGCCATCTCCGAGAG	195	102	30	168	118	55	172	108	30	H	TKT	NM_001064
GGCCATCTCTTCCTCAG	349	307	202	317	346	173	277	254	121	H	YWHAQ	NM_006826
AGGCTGTGTTCCTCCGT	16	39	11	34	67	22	26	38	8	I	ACY1	NM_000666
TGCCTCTGCGGGGCAGG	446	649	427	399	664	424	501	462	317	I	CD151	NM_004357
GGCACAGTAAAGGTGGC	175	216	142	332	350	173	456	316	204	I	CUEDC2	NM_024040
TCACACAGTGCCTGTCG	49	71	7	30	47	15	34	66	4	I	CXCR7	NM_001047841
TGTGAGGGAAGCTGCTT	53	87	15	67	102	52	52	90	42	I	FKBP10	BC016467
TGCTTTGCTTCATTCTG	28	63	26	22	79	26	49	118	61	I	GRB10	NM_005311
GTACTGTATGCTTGCCA	170	212	82	134	153	88	123	188	113	I	KPNB1‡‡	NM_002265
GTGGCAGTGGCCAGTTG	106	193	97	123	173	96	94	137	76	I	N/A	ENSG00000138744
GGGGAGCCCCGGGCCCG	61	63	26	30	51	18	34	57	0	I	NAT14	NM_020378
TGTTCAGGACCCTCCCT	28	67	26	60	63	26	60	28	0	I	NELF	NM_015537
TTTTCCTGGGGATCCTC	41	130	15	37	87	33	56	104	45	I	PCOTH	NM_001014442
GAAACCCGGTAGTCTAG	41	75	4	37	75	26	52	151	30	I	PLCB4	NM_000933
GTCTGACCCCAGGCCCC	126	205	82	119	193	103	157	179	38	I	PPP2R1A	NM_014225
GGCCCGAGTTACTTTTC	231	150	75	161	232	136	142	160	45	I	RPL35A††	NM_000996
GTTCGTGCCAAATTCCG	881	696	390	1100	712	523	497	782	461	I	RPL35A‡‡	NM_000996
TTACCATATCAAGCTGA	877	535	311	1130	598	405	636	791	578	I	RPL39‡‡	NM_001000
GCTGCAGCACAAGCGGC	268	244	127	45	216	125	157	71	11	I	RPS18††	NM_022551
AGCTCTTGGAGGCACCA	203	319	206	142	421	243	269	259	162	I	SELENBP1	NM_003944
TGCTGGTGTGTAAGGGG	69	102	45	82	87	37	105	75	30	I	SH3BP5L	NM_030645
GAGAGTAACAGGCCTGC	191	150	71	112	181	111	108	165	64	I	SYNC1	NM_030786
CTGAAAACCACTCAAAC	394	508	225	306	547	236	310	381	200	I	TFPI	NM_006287
TAAAAAAGGTTTCATCC	183	248	127	86	130	66	142	268	87	I	TFPI	NM_006287
CTCCCTCCTCTCCTACC	28	32	4	30	39	7	71	24	0	I	TK1	NM_003258
CATTTTCTAATTTTGTG	544	744	236	407	771	181	288	664	185	J	N/A	No map
TGATTTCACTTCCACTC	3480	5260	3910	3700	6110	3590	3040	5960	2600	K	MT-CO3	ENSG00000198938
TTTCTGTCTGGGGAAGG	130	236	82	123	201	111	101	188	113	K	PIK3CD	NM_005026
GCCGCTACTTCAGGAGC	256	370	199	224	330	169	142	316	38	K	RAMP1	NM_005855
ATGGTTACACTTTTGGT	93	161	94	75	208	118	60	226	95	K	UTX	NM_021140
CACTACTCACCAGACGC	2820	3900	3020	2740	4290	2440	2620	3120	1260	K	VPS13B††	ENSG00000132549
CTAAGACTTCACCAGTC	7120	11000	9730	6390	10900	8330	3610	8870	7850	L	N/A	ENSG00000210082

* Statistics according to the Audic and Claverie test statistic (p ≤ 0.05)
† Tag count per 1 million = (observed tag count/total tags in the library) × 1,000,000
‡ Trends are visually represented from A to P in Additional file 1, Figure S3. In addition to p-value considerations, significantly different trends were also required to display uniform directions of change in each biological replicate.
§ AS, Androgen-sensitive
II RAD, Responsive to androgen-deprivation
¶ CR, Castration-recurrent
** Human Genome Nomenclature Committee (HGNC)-approved gene names were used when possible. Non-HGNC-approved gene names were not italicized.
†† Tag maps antisense to gene
‡‡ Gene is known to display this expression trend in castration-recurrence
§§ Accession numbers were displayed following the priority (where available): RefSeq > Mammalian Gene Collection > Ensembl Gene. If the tag mapped to more than one transcript variant of the same gene, the accession number of the lowest numerical transcript variant was displayed.

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ISSN: 1755-8794

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