Dataset: Whole-transcript expression data for liposarcoma

Liposarcoma is the most common soft tissue sarcoma, accounting for about 20% of cases. Liposarcoma is classified into 5 histologic...

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Liposarcoma is the most common soft tissue sarcoma, accounting for about 20% of cases. Liposarcoma is classified into 5 histologic subtypes that fall into 3 biological groups characterized by specific genetic alterations. To identify genes that contribute to liposarcomagenesis and to better predict outcome for patients with the disease, we undertook expression profiling of liposarcoma. U133A expression profiling was performed on 140 primary liposarcoma samples, which were randomly split into training set (n=95) and test set (n=45). A multi-gene predictor for distant recurrence-free survival (DRFS) was developed using the supervised principal component method. Expression levels of the 588 genes in the predictor were used to calculate a risk score for each patient. In validation of the predictor in the test set, patients with low risk score had a 3-year DRFS of 83% vs. 45% for high risk score patients (P=0.001). The hazard ratio for high vs. low score, adjusted for histologic subtype, was 4.42 (95% confidence interval 1.26-15.55; P=0.021). The concordance probability for risk score was 0.732. Genes related to adipogenesis, DNA replication, mitosis, and spindle assembly checkpoint control were all highly represented in the multi-gene predictor. Three genes from the predictor, TOP2A, PTK7, and CHEK1, were found to be overexpressed in liposarcoma samples of all five subtypes and in liposarcoma cell lines. Knockdown of these genes in liposarcoma cell lines reduced proliferation and invasiveness and increased apoptosis. Thus, genes identified from this predictor appear to have roles in liposarcomagenesis and have promise as therapeutic targets. In addition, the multi-gene predictor will improve risk stratification for individual patients with liposarcoma. 140 human liposarcoma specimens were profiled on Affymetrix U133A arrays per manufacturer's instructions.

Species:: human
Samples:: 140
Source:: E-GEOD-30929
PubMed:: 21335544
Updated:: Dec.12, 2014
Registered:: Jun.18, 2014

Factors: (via ArrayExpress)

Sample	SAMPLE ID	SUBTYPE	DRFS	TRAININGTEST	TT.DRFS
GSM766672	WD0429	well-differentiated	FALSE	Test	36.11
GSM76667	WD9370	well-differentiated	FALSE	Test	26.48
GSM766670	WD9343	well-differentiated	FALSE	Training	27.27
GSM766669	WD725	well-differentiated	FALSE	Training	4.70
GSM766668	WD724	well-differentiated	FALSE	Training	6.28
GSM766667	WD721	well-differentiated	FALSE	Training	2.27
GSM766666	WD706	well-differentiated	FALSE	Training	43.76
GSM766665	WD705	well-differentiated	FALSE	Test	18.92
GSM766664	WD701	well-differentiated	FALSE	Test	12.06
GSM766663	WD696	well-differentiated	FALSE	Test	38.14
GSM766662	WD691	well-differentiated	FALSE	Training	18.60
GSM76666	WD688	well-differentiated	FALSE	Training	18.07
GSM766660	WD687	well-differentiated	FALSE	Training	13.86
GSM766659	WD6233	well-differentiated	FALSE	Training	34.66
GSM766658	WD60	well-differentiated	FALSE	Training	70.93
GSM766657	WD589	well-differentiated	FALSE	Test	39.00
GSM766656	WD5700	well-differentiated	FALSE	Training	32.56
GSM766655	WD558	well-differentiated	FALSE	Training	26.55
GSM766654	WD510	well-differentiated	FALSE	Training	54.37
GSM766653	WD4994	well-differentiated	FALSE	Training	33.61
GSM766652	WD499	well-differentiated	FALSE	Training	54.41
GSM76665	WD472	well-differentiated	FALSE	Training	59.66
GSM766650	WD468	well-differentiated	FALSE	Training	69.95
GSM766649	WD463	well-differentiated	FALSE	Test	72.97
GSM766648	WD459	well-differentiated	FALSE	Test	73.43
GSM766647	WD450	well-differentiated	TRUE	Training	58.22
GSM766646	WD426	well-differentiated	FALSE	Training	140.78
GSM766645	WD419	well-differentiated	FALSE	Training	127.18
GSM766644	WD418	well-differentiated	FALSE	Training	47.21
GSM766643	WD410	well-differentiated	FALSE	Training	39.66
GSM766642	WD380	well-differentiated	TRUE	Training	40.05
GSM76664	WD375	well-differentiated	FALSE	Test	44.06
GSM766640	WD368	well-differentiated	TRUE	Test	17.54
GSM766639	WD359	well-differentiated	FALSE	Training	61.27
GSM766638	WD356	well-differentiated	FALSE	Training	65.87
GSM766637	WD286	well-differentiated	FALSE	Training	43.07
GSM766636	WD221	well-differentiated	TRUE	Training	19.68
GSM766635	WD200	well-differentiated	TRUE	Training	0.36
GSM766634	WD199	well-differentiated	FALSE	Training	67.06
GSM766633	WD194	well-differentiated	FALSE	Training	58.64
GSM766632	WD0611	well-differentiated	FALSE	Training	36.73
GSM76663	WD702	well-differentiated	FALSE	Test	7.20
GSM766630	WD700	well-differentiated	FALSE	Training	68.01
GSM766629	WD444	well-differentiated	FALSE	Test	45.14
GSM766628	ALT500	well-differentiated	FALSE	Training	57.23
GSM766627	ALT497	well-differentiated	FALSE	Test	52.17
GSM766626	ALT486	well-differentiated	FALSE	Training	48.13
GSM766625	ALT479	well-differentiated	FALSE	Test	75.07
GSM766624	ALT476	well-differentiated	FALSE	Training	49.74
GSM766623	WD72	well-differentiated	FALSE	Test	51.75
GSM766622	WD602	well-differentiated	TRUE	Test	23.03
GSM76662	WD401	well-differentiated	TRUE	Test	37.39
GSM766620	PL9313	pleomorphic	FALSE	Test	38.14
GSM766619	PL640	pleomorphic	TRUE	Training	12.39
GSM766618	PL634	pleomorphic	FALSE	Training	24.74
GSM766617	PL627	pleomorphic	FALSE	Training	21.55
GSM766616	PL625	pleomorphic	TRUE	Training	5.91
GSM766615	PL619	pleomorphic	FALSE	Training	28.25
GSM766614	PL617	pleomorphic	TRUE	Test	10.64
GSM766613	PL4580	pleomorphic	TRUE	Training	23.95
GSM766612	PL3275	pleomorphic	FALSE	Training	31.44
GSM7666	PL299	pleomorphic	TRUE	Test	6.01
GSM766610	PL295	pleomorphic	FALSE	Training	116.21
GSM766609	PL289	pleomorphic	TRUE	Training	158.62
GSM766608	PL278	pleomorphic	FALSE	Training	51.02
GSM766607	PL269	pleomorphic	TRUE	Training	33.28
GSM766606	PL268	pleomorphic	TRUE	Training	8.87
GSM766605	PL247	pleomorphic	TRUE	Test	32.53
GSM766604	PL131	pleomorphic	TRUE	Training	6.01
GSM766603	PL130	pleomorphic	TRUE	Training	20.21
GSM766602	PL128	pleomorphic	TRUE	Training	7.43
GSM76660	PL126	pleomorphic	FALSE	Test	59.60
GSM766600	ML593	myxoid	FALSE	Test	34.33
GSM766599	ML709	myxoid	FALSE	Training	1.45
GSM766598	ML708	myxoid	FALSE	Training	7.13
GSM766597	ML622	myxoid	FALSE	Training	6.05
GSM766596	ML618	myxoid	FALSE	Test	25.82
GSM766595	ML414	myxoid	FALSE	Test	47.34
GSM766594	ML304	myxoid	FALSE	Training	57.46
GSM766593	ML298	myxoid	FALSE	Training	114.20
GSM766592	ML283	myxoid	TRUE	Training	46.55
GSM76659	ML257	myxoid	FALSE	Test	45.73
GSM766590	ML169	myxoid	FALSE	Training	61.73
GSM766589	ML165	myxoid	FALSE	Training	70.47
GSM766588	ML163	myxoid	FALSE	Training	73.30
GSM766587	ML161	myxoid	FALSE	Training	62.65
GSM766586	ML292	myxoid	TRUE	Test	52.07
GSM766585	ML253	myxoid	FALSE	Test	133.09
GSM766584	ML138	myxoid	TRUE	Test	0.69
GSM766583	MRC676	myxoid/round cell	FALSE	Test	15.93
GSM766582	MRC643	myxoid/round cell	FALSE	Training	20.53
GSM76658	MRC608	myxoid/round cell	TRUE	Training	1.77
GSM766580	MRC288	myxoid/round cell	FALSE	Training	47.90
GSM766579	MRC275	myxoid/round cell	TRUE	Training	104.44
GSM766578	MRC239	myxoid/round cell	TRUE	Test	12.12
GSM766577	MRC139	myxoid/round cell	FALSE	Test	56.67
GSM766576	MRC644	myxoid/round cell	FALSE	Training	17.51
GSM766575	MRC626	myxoid/round cell	FALSE	Training	25.03
GSM766574	MRC624	myxoid/round cell	TRUE	Training	3.45
GSM766573	MRC5397	myxoid/round cell	FALSE	Test	36.11
GSM766572	DD3516	dedifferentiated	TRUE	Test	3.71
GSM76657	WD432	dedifferentiated	TRUE	Training	30.65
GSM766570	PL243	dedifferentiated	TRUE	Training	3.84
GSM766569	WD439	dedifferentiated	FALSE	Training	39.36
GSM766568	DD88	dedifferentiated	TRUE	Test	32.39
GSM766567	DD8379	dedifferentiated	TRUE	Training	32.89
GSM766566	DD7533	dedifferentiated	TRUE	Test	8.48
GSM766565	DD719	dedifferentiated	FALSE	Test	3.68
GSM766564	DD718	dedifferentiated	FALSE	Training	4.70
GSM766563	DD715	dedifferentiated	TRUE	Test	7.26
GSM766562	DD714	dedifferentiated	TRUE	Training	3.38
GSM76656	DD712	dedifferentiated	FALSE	Training	3.32
GSM766560	DD69	dedifferentiated	FALSE	Training	61.27
GSM766559	DD672	dedifferentiated	TRUE	Training	41.13
GSM766558	DD670	dedifferentiated	FALSE	Training	52.01
GSM766557	DD668	dedifferentiated	TRUE	Training	8.31
GSM766556	DD639	dedifferentiated	TRUE	Training	29.80
GSM766555	DD6213	dedifferentiated	TRUE	Training	7.89
GSM766554	DD611	dedifferentiated	TRUE	Training	2.79
GSM766553	DD610	dedifferentiated	TRUE	Training	23.82
GSM766552	DD597	dedifferentiated	TRUE	Test	9.30
GSM76655	DD595	dedifferentiated	FALSE	Test	37.78
GSM766550	DD513	dedifferentiated	TRUE	Training	1.94
GSM766549	DD506	dedifferentiated	TRUE	Test	3.29
GSM766548	DD474	dedifferentiated	FALSE	Training	72.74
GSM766547	DD456	dedifferentiated	FALSE	Training	57.17
GSM766546	DD454	dedifferentiated	FALSE	Test	42.32
GSM766545	DD442	dedifferentiated	FALSE	Training	39.98
GSM766544	DD391	dedifferentiated	FALSE	Test	52.07
GSM766543	DD382	dedifferentiated	TRUE	Training	2.50
GSM766542	DD344	dedifferentiated	TRUE	Training	16.82
GSM76654	DD330	dedifferentiated	FALSE	Training	120.77
GSM766540	DD226	dedifferentiated	TRUE	Training	33.94
GSM766539	DD216	dedifferentiated	TRUE	Test	5.88
GSM766538	DD188	dedifferentiated	FALSE	Training	58.97
GSM766537	DD176	dedifferentiated	FALSE	Training	54.70
GSM766536	DD172	dedifferentiated	TRUE	Training	3.88
GSM766535	DD112	dedifferentiated	TRUE	Training	4.24
GSM766534	DD103	dedifferentiated	FALSE	Test	73.89
GSM766533	DD0728	dedifferentiated	FALSE	Training	32.95