Analyse - microRNA Survival Result | CGGA - Chinese Glioma Genome Altas

Analyse result - microRNA data (survival)

Dataset:

microRNA_array_198

Gene:

hsa-miR-181d

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Data
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CGGA.ID	PRS.type	Histology	Grade	Gender	Age	OS	Censor	Expression
CGGA_253	Primary	A	WHO II	Female	37	5159	0	475.7871
CGGA_258	Primary	A	WHO II	Female	61	663	1	-10.71934
CGGA_281	Primary	A	WHO II	Female	36	1236	0	101.3922
CGGA_285	Primary	A	WHO II	Male	30	1576	0	126.2377
CGGA_316	Primary	A	WHO II	Female	30	4682	0	1462.289
CGGA_317	Primary	A	WHO II	Female	42	4681	0	1385.259
CGGA_321	Primary	A	WHO II	Male	42	NA	NA	355.4094
CGGA_357	Primary	A	WHO II	Female	37	2518	1	416.0789
CGGA_365	Primary	A	WHO II	Female	32	3593	0	646.6498
CGGA_379	Primary	A	WHO II	Female	39	1077	1	35.58109
CGGA_396	Primary	A	WHO II	Female	49	4576	0	11.33216
CGGA_399	Primary	A	WHO II	Male	36	2663	1	399.6841
CGGA_402	Primary	AA	WHO III	Male	53	4562	0	157.8558
CGGA_407	Primary	A	WHO II	Male	33	4555	0	480.8643
CGGA_433	Primary	A	WHO II	Male	30	NA	NA	-91.24295
CGGA_434	Primary	A	WHO II	Male	35	4513	0	1493.551
CGGA_447	Primary	A	WHO II	Female	20	4508	0	306.2721
CGGA_459	Primary	A	WHO II	Male	44	3613	0	990.727
CGGA_461	Primary	A	WHO II	Male	36	1266	1	12.36649
CGGA_469	Primary	A	WHO II	Male	30	4464	0	253.5339
CGGA_505	Primary	A	WHO II	Male	36	2994	1	-35.29445
CGGA_522	Primary	A	WHO II	Female	24	3630	0	89.47379
CGGA_542	Primary	A	WHO II	Male	24	NA	NA	173.4008
CGGA_544	Primary	A	WHO II	Female	44	4371	0	302.0789
CGGA_548	Primary	A	WHO II	Male	39	NA	NA	524.4952
CGGA_552	Primary	A	WHO II	Female	36	4362	0	265.2721
CGGA_590	Primary	A	WHO II	Male	36	4319	0	1546.349
CGGA_592	Primary	A	WHO II	Male	47	4315	0	-24.55196
CGGA_595	Primary	A	WHO II	Female	51	NA	NA	-3.071275
CGGA_601	Primary	A	WHO II	Male	36	1133	1	2647.852
CGGA_626	Primary	A	WHO II	Male	20	4273	0	130.9802
CGGA_648	Primary	A	WHO II	Female	33	3647	1	435.0575
CGGA_663	Primary	A	WHO II	Female	29	4210	0	554.521
CGGA_673	Primary	AA	WHO III	Male	54	NA	NA	307.7828
CGGA_688	Primary	A	WHO II	Male	19	4196	0	1.379368
CGGA_692	Primary	AOA	WHO III	Male	19	NA	NA	1270.714
CGGA_708	Primary	A	WHO II	Female	38	4167	0	1358.328
CGGA_711	Primary	A	WHO II	Male	49	1798	0	449.8858
CGGA_712	Primary	A	WHO II	Male	25	NA	NA	519.3879
CGGA_718	Primary	A	WHO II	Male	17	4159	0	146.0832
CGGA_736	Primary	A	WHO II	Male	38	1164	1	-5.54767
CGGA_743	Primary	A	WHO II	Male	30	851	1	582.5339
CGGA_746	Primary	A	WHO II	Male	45	332	1	530.0875
CGGA_753	Primary	A	WHO II	Male	24	3217	1	27.3622
CGGA_767	Primary	AA	WHO III	Male	36	1310	1	47.57679
CGGA_770	Primary	A	WHO II	Male	30	1057	0	1046.053
CGGA_776	Primary	A	WHO II	Female	48	4091	0	1827.8
CGGA_781	Recurrent	rA	WHO II	Male	35	4088	0	45.48666
CGGA_792	Primary	A	WHO II	Male	32	816	1	814.903
CGGA_275	Primary	O	WHO II	Female	43	4722	0	109.5596
CGGA_323	Primary	O	WHO II	Female	48	4338	0	149.6412
CGGA_387	Primary	O	WHO II	Female	51	539	1	-31.65067
CGGA_446	Primary	O	WHO II	Female	35	4508	0	12.77851
CGGA_484	Primary	O	WHO II	Female	32	4442	0	14.49954
CGGA_485	Primary	O	WHO II	Male	31	2437	0	-85.91248
CGGA_543	Primary	O	WHO II	Male	43	4371	0	949.9673
CGGA_579	Primary	O	WHO II	Female	42	2125	1	17.59396
CGGA_589	Primary	O	WHO II	Male	33	4320	0	13.51671
CGGA_633	Primary	O	WHO II	Female	56	1812	1	1128.388
CGGA_639	Primary	O	WHO II	Male	47	4256	0	1197.139
CGGA_659	Primary	O	WHO II	Female	50	730	0	-1.551962
CGGA_672	Primary	O	WHO II	Male	22	4215	0	1100.045
CGGA_41	Primary	AA	WHO III	Male	53	94	1	33.02744
CGGA_202	Primary	AA	WHO III	Male	41	NA	NA	20.86006
CGGA_247	Primary	AA	WHO III	Male	60	609	1	895.7742
CGGA_249	Primary	AA	WHO III	Male	41	312	1	508.0875
CGGA_331	Primary	AA	WHO III	Female	27	1638	1	900.5381
CGGA_334	Primary	AA	WHO III	Female	35	1450	1	874.2892
CGGA_353	Primary	AA	WHO III	Female	60	516	1	693.0446
CGGA_354	Primary	AA	WHO III	Male	62	180	1	939.0017
CGGA_405	Primary	AA	WHO III	Male	59	497	1	1462.289
CGGA_410	Primary	AA	WHO III	Female	70	1099	1	674.1691
CGGA_412	Primary	AA	WHO III	Female	42	358	1	885.4308
CGGA_476	Primary	A	WHO II	Female	37	936	1	696.5554
CGGA_486	Primary	AA	WHO III	Male	23	424	1	68.28924
CGGA_260	Primary	AO	WHO III	Female	49	567	1	778.1948
CGGA_277	Primary	AO	WHO III	Male	40	4739	0	65.81714
CGGA_314	Recurrent	rAO	WHO III	Male	39	2568	1	440.9159
CGGA_364	Primary	AO	WHO III	Male	32	666	1	1164.628
CGGA_403	Primary	AO	WHO III	Male	43	925	0	839.3279
CGGA_414	Primary	AO	WHO III	Male	28	4541	0	390.0703
CGGA_474	Primary	AO	WHO III	Male	NA	2029	0	221.2721
CGGA_481	Primary	AO	WHO III	Female	61	1507	1	1212.165
CGGA_489	Primary	AO	WHO III	Male	31	3804	0	869.5596
CGGA_490	Primary	AO	WHO III	Female	37	3804	0	1128.388
CGGA_508	Primary	AO	WHO III	Female	17	285	1	2291.075
CGGA_558	Primary	AO	WHO III	Male	34	188	0	33.74847
CGGA_598	Primary	AO	WHO III	Female	61	3677	1	1366.903
CGGA_231	Primary	AA	WHO III	Male	60	510	1	900.5381
CGGA_232	Recurrent	rAA	WHO III	Male	28	415	1	104.8515
CGGA_259	Recurrent	rAA	WHO III	Female	26	649	0	1228.568
CGGA_279	Recurrent	rAA	WHO III	Female	49	1314	1	949.9673
CGGA_329	Primary	AA	WHO III	Male	42	419	1	497.2678
CGGA_336	Recurrent	rAO	WHO III	Female	57	2549	1	660.1691
CGGA_351	Primary	AA	WHO III	Female	35	742	1	967.1691
CGGA_352	Primary	AA	WHO III	Male	18	4639	0	874.2892
CGGA_391	Primary	AOA	WHO III	Female	29	2010	1	1106.834
CGGA_393	Primary	AOA	WHO III	Male	65	2190	1	955.6068
CGGA_406	Recurrent	rAA	WHO III	Female	24	90	1	900.5381
CGGA_438	Primary	AOA	WHO III	Male	53	686	1	-20.32879
CGGA_471	Primary	AA	WHO III	Male	45	1373	1	285.933
CGGA_487	Recurrent	rGBM	WHO IV	Male	46	156	1	650.3622
CGGA_492	Recurrent	rAA	WHO III	Male	27	652	0	-6.002606
CGGA_498	Primary	AOA	WHO III	Male	37	356	1	-10.22578
CGGA_513	Primary	AA	WHO III	Female	44	1374	1	885.4308
CGGA_562	Primary	AA	WHO III	Female	62	290	1	1280.13
CGGA_596	Primary	AA	WHO III	Male	60	1618	1	667.4695
CGGA_1	Primary	GBM	WHO IV	Female	43	605	1	508.0875
CGGA_11	Primary	GBM	WHO IV	Female	57	155	1	-104.0284
CGGA_13	Primary	GBM	WHO IV	Male	59	267	1	96.16907
CGGA_24	Primary	GBM	WHO IV	Male	48	387	1	233.3365
CGGA_58	Primary	GBM	WHO IV	Male	60	570	1	188.8643
CGGA_88	Primary	GBM	WHO IV	Male	20	169	1	-53.98544
CGGA_100	Primary	GBM	WHO IV	Male	47	335	1	11.33216
CGGA_102	Primary	GBM	WHO IV	Male	17	214	1	217.8257
CGGA_124	Primary	GBM	WHO IV	Male	53	414	1	-16.30733
CGGA_126	Primary	GBM	WHO IV	Female	50	1177	1	516.5854
CGGA_139	Primary	GBM	WHO IV	Male	59	694	1	-24.55196
CGGA_144	Primary	GBM	WHO IV	Male	54	363	1	258.7871
CGGA_156	Primary	GBM	WHO IV	Male	51	179	1	-32.15282
CGGA_160	Primary	OA	WHO II	Female	29	4982	0	494.6068
CGGA_161	Primary	GBM	WHO IV	Female	35	329	1	27.3622
CGGA_168	Primary	GBM	WHO IV	Male	17	3086	0	234.6583
CGGA_169	Primary	GBM	WHO IV	Male	59	450	1	272.6197
CGGA_172	Primary	GBM	WHO IV	Female	57	462	1	124.1047
CGGA_178	Primary	GBM	WHO IV	Male	38	972	1	-17.11849
CGGA_182	Primary	GBM	WHO IV	Female	47	128	1	227.903
CGGA_188	Primary	GBM	WHO IV	Male	51	397	1	530.0875
CGGA_195	Primary	GBM	WHO IV	Male	48	486	1	-60.16999
CGGA_203	Primary	GBM	WHO IV	Male	40	188	1	548.066
CGGA_205	Primary	GBM	WHO IV	Male	65	292	1	-45.87385
CGGA_210	Primary	GBM	WHO IV	Female	68	300	1	-46.27299
CGGA_214	Primary	GBM	WHO IV	Female	48	193	1	519.3879
CGGA_218	Primary	GBM	WHO IV	Male	12	313	1	539.0446
CGGA_221	Primary	GBM	WHO IV	Male	37	287	1	14.96735
CGGA_222	Primary	GBM	WHO IV	Male	51	520	1	-16.30733
CGGA_225	Primary	GBM	WHO IV	Male	32	1741	1	1093.1
CGGA_238	Primary	GBM	WHO IV	Male	53	275	1	905.8257
CGGA_240	Primary	GBM	WHO IV	Male	54	386	1	864.8815
CGGA_242	Primary	GBM	WHO IV	Male	62	382	1	374.7957
CGGA_255	Primary	GBM	WHO IV	Female	42	591	1	57.49954
CGGA_264	Primary	GBM	WHO IV	Male	54	383	1	456.7184
CGGA_287	Primary	GBM	WHO IV	Female	39	571	1	285.933
CGGA_292	Primary	GBM	WHO IV	Male	37	812	1	650.3622
CGGA_306	Primary	GBM	WHO IV	Male	59	901	1	196.8901
CGGA_308	Primary	GBM	WHO IV	Female	55	823	1	681.5253
CGGA_311	Primary	GBM	WHO IV	Male	40	230	1	717.6154
CGGA_324	Primary	GBM	WHO IV	Male	52	336	1	569.2806
CGGA_335	Primary	GBM	WHO IV	Male	59	385	1	657.1948
CGGA_342	Primary	GBM	WHO IV	Female	49	500	1	486.1776
CGGA_345	Primary	GBM	WHO IV	Female	43	1547	0	755.8901
CGGA_346	Primary	GBM	WHO IV	Male	45	104	1	312.521
CGGA_349	Primary	GBM	WHO IV	Female	49	869	0	311.0017
CGGA_366	Primary	GBM	WHO IV	Male	54	255	1	634.9073
CGGA_370	Primary	GBM	WHO IV	Male	51	338	1	385.9888
CGGA_371	Primary	GBM	WHO IV	Male	42	811	1	530.0875
CGGA_373	Primary	GBM	WHO IV	Female	45	281	1	146.0832
CGGA_375	Primary	GBM	WHO IV	Male	57	657	1	454.1734
CGGA_377	Primary	GBM	WHO IV	Male	17	398	1	367.7399
CGGA_380	Primary	GBM	WHO IV	Male	52	165	1	436.9974
CGGA_401	Primary	GBM	WHO IV	Female	24	168	1	27.3622
CGGA_409	Primary	GBM	WHO IV	Male	63	98	1	424.4566
CGGA_419	Primary	GBM	WHO IV	Male	56	198	1	513.7485
CGGA_436	Primary	GBM	WHO IV	Male	48	955	1	650.3622
CGGA_437	Primary	GBM	WHO IV	Female	54	1025	1	730.6068
CGGA_439	Primary	GBM	WHO IV	Female	33	3813	1	769.4266
CGGA_442	Primary	GBM	WHO IV	Male	62	1555	1	922.0875
CGGA_444	Primary	GBM	WHO IV	Female	70	225	1	536.1433
CGGA_451	Primary	GBM	WHO IV	Male	61	795	1	646.6498
CGGA_454	Primary	GBM	WHO IV	Male	37	412	1	709.6154
CGGA_464	Primary	GBM	WHO IV	Female	39	403	1	657.1948
CGGA_504	Primary	GBM	WHO IV	Female	22	563	1	944.4609
CGGA_512	Primary	GBM	WHO IV	Male	33	4371	0	557.3493
CGGA_525	Primary	GBM	WHO IV	Male	61	138	1	463.8772
CGGA_527	Primary	GBM	WHO IV	Male	33	439	1	1008.959
CGGA_547	Primary	GBM	WHO IV	Male	29	1337	1	1375.916
CGGA_549	Primary	GBM	WHO IV	Female	34	413	1	685.4352
CGGA_557	Primary	GBM	WHO IV	Female	38	257	1	563.4695
CGGA_570	Primary	GBM	WHO IV	Female	60	3602	0	713.3493
CGGA_573	Primary	GBM	WHO IV	Male	35	946	1	554.521
CGGA_575	Primary	GBM	WHO IV	Male	55	551	1	541.9587
CGGA_588	Primary	GBM	WHO IV	Male	58	773	1	557.3493
CGGA_593	Primary	GBM	WHO IV	Male	37	242	1	572.418
CGGA_594	Primary	GBM	WHO IV	Female	27	4318	0	627.7056
CGGA_597	Primary	GBM	WHO IV	Female	31	733	1	869.5596
CGGA_604	Primary	GBM	WHO IV	Male	46	381	1	403.8815
CGGA_606	Primary	GBM	WHO IV	Male	62	325	1	721.4867
CGGA_609	Primary	GBM	WHO IV	Female	44	512	0	725.7957
CGGA_612	Primary	GBM	WHO IV	Male	47	2023	1	864.8815
CGGA_9	Recurrent	rGBM	WHO IV	Male	43	408	1	371.2892
CGGA_81	Recurrent	rGBM	WHO IV	Male	39	551	1	1526.757
CGGA_104	Secondary	sGBM	WHO IV	Male	27	440	0	145.1691
CGGA_220	Secondary	sGBM	WHO IV	Male	34	318	1	638.2249
CGGA_462	Secondary	sGBM	WHO IV	Male	38	361	1	595.2291
CGGA_518	Secondary	sGBM	WHO IV	Male	27	212	1	1315.088
CGGA_545	Recurrent	rGBM	WHO IV	Female	38	555	1	747.727
CGGA_822	Secondary	sGBM	WHO IV	Male	46	2237	1	1654.534
CGGA_D59	Secondary	sGBM	WHO IV	Female	30	NA	NA	318.7957

data.file<-"data.txt"
gene<-"hsa-miR-181d"

## load R package
library(survminer)
library(survival)
library(ggpubr)
library(gridExtra)

## import data
dat<-read.table(data.file, sep='\t', head=T)
rownames(dat)<-dat$CGGA.ID
#head(dat)
mat<-dat[!is.na(dat$PRS.type)&(dat$PRS.type=="Primary"|dat$PRS.type=="Recurrent")&
           !is.na(dat$Grade)&
           !is.na(dat$OS)&
           !is.na(dat$Censor),]

### all grade - Primary ###
matt<-mat[mat$PRS.type=='Primary',]
med.microRNA<-median(matt$Expression)
more.med.microRNA.index<-which(matt$Expression>=med.microRNA)
less.med.microRNA.index<-which(matt$Expression< med.microRNA)
matt$status<-NA
matt$status[more.med.microRNA.index]<-paste0('High (',length(more.med.microRNA.index),')')
matt$status[less.med.microRNA.index]<-paste0('Low (',length(less.med.microRNA.index),')')