Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays

Srinivasan, Subhashini; Patil, Arun H; Verma, Mohit; Bingham, Jonathan L; Srivatsan, Raghunathan

doi:10.1186/2043-9113-2-21

Journal of Clinical Bioinformatics

Table 4 Splice events up-and down-regulated in a tumor specific fashion with a p-value of < 0.0001

From: Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays

Sl.No	Gene name	Source of evidence	Are they from alt. splicing region?	P-value	Fold-change (log2)	Base level expression around splice sites
1	TARP	BC105589.J1-2	TRUE	9.08E-05	1.65501	✓
2	SH3RF1	NM_020870.J11-12.	FALSE	2.32E-05	1.602221	-
3	PPP3CA	NM_000944.J5-6	TRUE	2.60E-05	1.52093	✓
4	MARCH6	NM_005885.J9-10	TRUE	2.48E-05	1.501025	-
5	ARFGAP3	NM_014570.J2-3	TRUE	6.28E-05	1.441878	✓
6	TAOK3	NM_016281.J18-19	FALSE	4.00E-05	1.379249	✓
7	EIF2AK4	NM_001013703.J37-38	TRUE	3.15E-06	1.346129	-
8	TMEM87A	NM_015497.J7-8	TRUE	3.81E-05	1.318233	✓
9	TOM1L1	NM_005486.J5-6	TRUE	1.14E-05	1.222369	✓
10	FERMT3	NT_033903.311.J10-11	FALSE	5.09E-05	1.211549	-
11	RPL7L1	NM_198486.J2-3	TRUE	4.14E-05	1.200866	-
12	TTC3	NM_003316.J18-19	TRUE	6.18E-05	1.183933	-
13	ACSL3	NM_004457.J12-13	TRUE	6.56E-05	1.158874	✓
14	SF3B1	NM_012433.J4-5	TRUE	8.85E-05	1.147913	✓
15	KLK3	BF372485.J1-2.	TRUE	8.13E-05	1.14738	-
16	CTBP2	NM_001083914.J2-3	TRUE	6.29E-05	1.114432	✓
17	SR140	NM_001080415.J25-26	TRUE	6.82E-05	1.109745	-
18	GTF3C1	NM_001520.J29-30	FALSE	5.11E-06	1.080653	-
19	CHEK1	NT_033899.609.J6-7	TRUE	6.83E-05	1.071581	✓
20	C15orf44	NM_030800.J11-12.	TRUE	2.45E-05	1.058924	-
21	CCDC14	NM_022757.J6-7	TRUE	1.26E-05	1.018248	-
22	KIAA0368	NM_001080398.J30-31	TRUE	6.62E-05	1.009773	✓
23	COPZ1,MIR148B	NM_016057.J3-4	TRUE	1.92E-05	1.001943	✓
24	ECH1,HNRNPL	NM_001533.J4-5	TRUE	1.64E-05	0.991637	✓
25	CNDP1	chr18.71.004.a.J2-3	TRUE	4.40E-05	0.97475	-
26	NULL	CN480760.J3-4	FALSE	5.32E-07	0.954029	✓
27	BCLAF1	NM_014739.J8-9	TRUE	2.87E-05	0.905132	✓
28	SON	NM_138927.J10-11	TRUE	2.17E-05	0.902497	✓
29	HSP90B1	NM_003299.J11-12	TRUE	1.11E-05	0.881922	✓
30	TTC19	NM_017775.J3-4	TRUE	8.24E-05	0.87852	-
31	TSPAN1	NM_005727.J6-7	TRUE	9.96E-05	0.873753	✓
32	NET1	NM_001047160.J6-7	TRUE	1.90E-06	0.869833	✓
33	ATXN10	NM_013236.J4-5	TRUE	8.27E-05	0.826939	✓
34	CANT1	NM_001159772.J3-4	TRUE	1.80E-05	0.793932	-
35	CCDC53	NM_016053.J3-4	TRUE	2.60E-05	0.780735	-
36	HADHA	NM_000182.J7-8	TRUE	8.58E-05	0.758566	-
37	CBS	NT_030188.38.J3-4	FALSE	4.96E-05	0.745529	-
38	SLTM	NM_024755.J4-5	TRUE	6.69E-05	0.675305	✓
39	DDX5	NM_004396.J3-4	TRUE	9.69E-05	0.671894	✓
40	HSPA8	BG699643.J2-3	TRUE	1.46E-05	0.609402	✓
41	LYNX1	NM_023946.J2-3	TRUE	4.67E-05	−1.56988	✓
42	KLHL29	NM_052920.J10-11	FALSE	7.16E-05	−1.33184	✓
43	ITGA3	NM_002204.J17-18	TRUE	1.59E-05	−1.23949	✓
44	CNN2	NM_004368.J6-7.	TRUE	2.77E-05	−1.19031	✓
45	SIN3A	NT_010194.1124.J12-13	FALSE	6.71E-05	−1.15772	✓
46	LAMA5	NM_005560.J78-79	FALSE	5.75E-05	−1.13839	✓
47	DPM2	NM_003863.J2-3	TRUE	2.18E-05	−1.11538	✓
48	PINK1	NM_032409.J6-7	TRUE	1.10E-05	−1.09024	✓
49	NCAPD2,SCARNA10	NT_009759.130.J28-29	FALSE	4.16E-05	−1.06536	-
50	EML2,MIR330	NM_012155.J17-18	FALSE	3.73E-05	−1.04227	✓
51	HEATR7A	NM_032450.J42-43	TRUE	5.59E-05	−0.97289	-
52	HEATR7A	NM_032450.J18-19	TRUE	1.80E-05	−0.96627	✓
53	ARAP1,STARD10	NM_001040118.J12-13	FALSE	6.18E-05	−0.95743	✓
54	ALS2CL	NM_147129.J15-16	FALSE	9.60E-05	−0.94678	✓
55	RAB25	chr1.155.009.a.J2-3	FALSE	2.75E-05	−0.91566	✓
56	NULL	NT_030188.20.J5-6	FALSE	5.90E-05	−0.88101	-
57	ATF6B,TNXB	NM_019105.J22-23	FALSE	9.19E-05	−0.85967	✓
58	RUVBL2	NM_006666.J11-12	FALSE	3.78E-05	−0.75383	✓
59	MAP3K12	NM_006301.J4-5	TRUE	6.44E-05	−0.72161	✓
60	AIFM2	NM_032797.J7-8	FALSE	2.12E-05	−0.72049	✓
61	ATP2A2	NM_001681.J19-20	FALSE	7.93E-05	−0.66293	✓

Back to article page