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