A microRNA expression signature of human solid tumors defines cancer gene targets -- Volinia et al. 103 (7): 2257 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Volinia et al. 10.1073/pnas.0510565103.

Supporting Information

Files in this Data Supplement:

Supporting Figure 4
Supporting Table 3
Supporting Table 4
Supporting Table 5
Supporting Table 6
Supporting Table 7
Supporting Table 8
Supporting Table 9
Supporting Table 10
Supporting Table 11
Supporting Table 12
Supporting Table 13
Supporting Table 14

Fig. 4. Unsupervised analysis of microRNA expression data. MicroRNA profiling of 540 samples covering breast, colon, lung, pancreas, prostate and stomach normal tissues and tumors were filtered, and centred and normalized for each feature. The data were subject to hierarchical clustering on both the samples (horizontally oriented) and the features (vertically oriented), with probe names on the left, with average-linkage and Pearson correlation as a similarity measure. Sample names are indicated on the top and miRNA names on the left. In parenthesis is indicated the probe ID, since the same microRNA can have been measured by different oligonucleotides.

Table 3. Samples used in the study (tumors and corresponding normals)

Tumor type	Cancer samples	Normal samples
Lung carcinoma	123	123
Breast carcinoma	79	6*
Colon carcinoma	46	8
Gastric carcinoma	20	21
Endocrine pancreatic tumours	39	12
Prostate cancer	56	7
All tissues	363	177

* Pools of five unrelated normal breast tissues each (for a total of 30 unrelated individuals)

Table 4. Deregulated microRNAs in solid common cancers

Cancer	PAM up-regulated	SAM up-regulated	PAM down-regulated	SAM down-regulated
Breast	15	3 (FDR=0.33)	12	47
Colon	21	42 (FDR<=0.06)	1	5
Lung	35	38 (FDR<=0.01)	3	3
Pancreas	55	50 (FDR<=0.01)	2	8
Stomach	22	22 (FDR=0.06)	6	4
Prostate	39	49 (FDR=0.06)	6	3

Prediction analysis of microarrays (PAM) identifies those genes which best characterize cancers and normal tissues, whilst significance analysis of microarrays (SAM) all those which have differential expression in the two classes. False detection rates computed in SAM (FDR) are indicated in parentheses.

Table 5. MicroRNAs selected by prediction analysis of microarray (PAM) in breast (cancer vs. normal tissues)

miRNA (ID)	Breast cancer score	Breast normal score
miR-21 (47)	0.0331	-0.4364
miR-29b-2 (95)	0.0263	-0.3467
miR-146 (144)	0.0182	-0.2391
miR-125b-2 (111)	-0.0174	0.2286
miR-125b-1 (109)	-0.0169	0.222
miR-10b (32)	-0.0164	0.2166
miR-145 (143)	-0.0158	0.2076
miR-181a (158)	0.0153	-0.201
miR-140 (136)	-0.0122	0.1613
miR-213 (160)	0.0116	-0.1527
miR-29a prec (63)	0.0109	-0.1441
miR-181b-1 (210)	0.0098	-0.1284
miR-199b (194)	0.0089	-0.1172
miR-29b-1 (64)	0.0084	-0.1111
miR-130a (120)	-0.0076	0.1001
miR-155 (157)	0.0072	-0.0951
let-7a-2 (3)	-0.0042	0.0554
miR-205 (201)	-0.004	0.0533
miR-29c (65)	0.0032	-0.0423
miR-224 (228)	-0.003	0.0399
miR-100 (91)	-0.0021	0.0283
miR-31 (73)	0.0017	-0.022
miR-30c (70)	-7.00E-04	0.009
miR-17-5p (41)	7.00E-04	-0.0089
miR-210 (205)	4.00E-04	-0.0057
miR-122a (101)	4.00E-04	-0.005
miR-16-2 (39)	-1.00E-04	0.0013

Twenty-seven miRs selected, misclassification error after cross validation of 0.08. Fifteen overexpressed miRs in cancer are indicated by positive cancer scores; 12 down-regulated miRs are indicated by negative cancer scores.

Table 6. MicroRNAs selected by prediction analysis of microarray (PAM) in colon (cancer vs. normal tissues)

miRNA (ID)	Colon cancer score	Colon normal score
miR-24-1 (52)	0.0972	-0.5589
miR-29b-2 (95)	0.0669	-0.3845
miR-20a (46)	0.0596	-0.3424
miR-10a (30)	0.0511	-0.2938
miR-32 (75)	0.0401	-0.2306
miR-203 (197)	0.0391	-0.2251
miR-106a (99)	0.0364	-0.2094
miR-17-5p (41)	0.0349	-0.2005
miR-30c (70)	0.0328	-0.1888
miR-223 (227)	0.0302	-0.1736
miR-126* (102)	0.0199	-0.1144
miR-128b (115)	0.0177	-0.102
miR-21 (47)	0.0162	-0.0929
miR-24-2 (54)	0.0145	-0.0835
miR-99b prec (88)	0.0125	-0.0721
miR-155 (157)	0.0092	-0.0528
miR-213 (160)	0.0091	-0.0522
miR-150 (148)	0.0042	-0.0243
miR-107 (100)	0.003	-0.0173
miR-191 (177)	0.0028	-0.0159
miR-221 (224)	0.002	-0.0116
miR-9-3 (28)	-0.0014	0.0083

Twenty-two miRs selected, misclassification error after cross validation of 0.09. Twenty-one overexpressed miRs in cancer are indicated by positive cancer scores; one down-regulated miR is indicated by negative cancer scores.

Table 7. MicroRNAs selected by prediction analysis of microarray (PAM) in lung (cancer vs. normal tissues)

miRNA (ID)	Lung cancer score	Lung normal score
miR-21 (47)	0.175	-0.175
miR-205 (201)	0.1317	-0.1317
miR-200b (195)	0.1127	-0.1127
miR-9-1 (24)	0.1014	-0.1014
miR-210 (205)	0.0994	-0.0994
miR-148 (146)	0.0737	-0.0737
miR-141 (137)	0.0631	-0.0631
miR-132 (121)	0.0586	-0.0586
miR-215 (213)	0.0575	-0.0575
miR-128b (115)	0.0559	-0.0559
let-7g (15)	0.0557	-0.0557
miR-16-2 (39)	0.0547	-0.0547
miR-129-1/2 prec (118)	0.0515	-0.0515
miR-126* (102)	-0.0406	0.0406
miR-142-as (139)	0.0366	-0.0366
miR-30d (72)	-0.0313	0.0313
miR-30a-5p (66)	-0.0297	0.0297
miR-7-2 (21)	0.0273	-0.0273
miR-199a-1 (191)	0.0256	-0.0256
miR-127 (112)	0.0254	-0.0254
miR-34a prec (79)	0.0214	-0.0214
miR-34a (78)	0.0188	-0.0188
miR-136 (130)	0.0174	-0.0174
miR-202 (196)	0.0165	-0.0165
miR-196-2 (188)	0.0134	-0.0134
miR-199a-2 (192)	0.0126	-0.0126
let-7a-2 (3)	0.0109	-0.0109
miR-124a-1 (104)	0.0081	-0.0081
miR-149 (147)	0.0079	-0.0079
miR-17-5p (41)	0.0061	-0.0061
miR-196-1 prec (186)	0.0053	-0.0053
miR-10a (30)	0.0049	-0.0049
miR-99b prec (88)	0.0045	-0.0045
miR-196-1 (185)	0.0044	-0.0044
miR-199b (194)	0.0039	-0.0039
miR-191 (177)	0.0032	-0.0032
miR-195 (184)	7.00E-04	-7.00E-04
miR-155 (157)	7.00E-04	-7.00E-04

Thirty-eight miRs selected, misclassification error after cross validation of 0.31. Thirty-five overexpressed miRs in cancer are indicated by positive cancer scores; three down-regulated miRs are indicated by negative cancer scores.

Table 8. MicroRNAs selected by prediction analysis of microarray (PAM) in pancreas (cancer vs. normal tissues)

miRNA (ID)	Pancreas cancer score	Pancreas normal score
miR-103-2 (96)	0.4746	-1.582
miR-103-1 (97)	0.4089	-1.3631
miR-24-2 (54)	0.4059	-1.3529
miR-107 (100)	0.3701	-1.2336
miR-100 (91)	0.3546	-1.182
miR-125b-2 (111)	0.3147	-1.0489
miR-125b-1 (109)	0.3071	-1.0237
miR-24-1 (52)	0.2846	-0.9488
miR-191 (177)	0.2661	-0.887
miR-23a (50)	0.2586	-0.8619
miR-26a-1 (56)	0.2081	-0.6937
miR-125a (107)	0.1932	-0.644
miR-130a (120)	0.1891	-0.6303
miR-26b (58)	0.1861	-0.6203
miR-145 (143)	0.1847	-0.6158
miR-221 (224)	0.177	-0.59
miR-126* (102)	0.1732	-0.5772
miR-16-2 (39)	0.1698	-0.5659
miR-146 (144)	0.1656	-0.552
miR-214 (212)	0.1642	-0.5472
miR-99b (89)	0.1636	-0.5454
miR-128b (115)	0.1536	-0.512
miR-155 (157)	-0.1529	0.5098
miR-29b-2 (95)	0.1487	-0.4956
miR-29a (62)	0.1454	-0.4848
miR-25 (55)	0.1432	-0.4775
miR-16-1 (38)	0.1424	-0.4746
miR-99a (90)	0.1374	-0.4581
miR-224 (228)	0.1365	-0.4549
miR-30d (72)	0.1301	-0.4336
miR-92-2 (82)	0.116	-0.3865
miR-199a-1 (191)	0.1158	-0.3861
miR-223 (227)	0.1141	-0.3803
miR-29c (65)	0.113	-0.3768
miR-30b (68)	0.1008	-0.3361
miR-129-1/2 (117)	0.1001	-0.3337
miR-197 (189)	0.0975	-0.325
miR-17-5p (41)	0.0955	-0.3185
miR-30c (70)	0.0948	-0.316
miR-7-1 (19)	0.0933	-0.311
miR-93-1 (83)	0.0918	-0.3061
miR-140 (136)	0.0904	-0.3015
miR-30a-5p (66)	0.077	-0.2568
miR-132 (121)	0.0654	-0.2179
miR-181b-1 (210)	0.0576	-0.1918
miR-152 prec (151)	-0.0477	0.1591
miR-23b (51)	0.0469	-0.1562
miR-20a (46)	0.0452	-0.1507
miR-222 (225)	0.0416	-0.1385
miR-27a (59)	0.0405	-0.1351
miR-92-1 (81)	0.0332	-0.1106
miR-21 (47)	0.0288	-0.0959
miR-129-1/2 prec (118)	0.0282	-0.0939
miR-150 (148)	0.0173	-0.0578
miR-32 (75)	0.0167	-0.0558
miR-106a (99)	0.0142	-0.0473
miR-29b-1 (64)	0.0084	-0.028

Fifty-seven miRs selected, misclassification error after cross validation of 0.02. Fifty-five overexpressed miRs in cancer are indicated by positive cancer scores; two down-regulated miRs are indicated by negative cancer scores.

Table 9. MicroRNAs selected by prediction analysis of microarray (PAM) in prostate (cancer vs. normal tissues)

miRNA (ID)	Prostate cancer score	Prostate normal score
let-7d (8)	0.0528	-0.4227
miR-128a prec (113)	-0.0412	0.3298
miR-195 (184)	0.04	-0.3199
miR-203 (197)	0.0356	-0.2851
let-7a-2 prec (2)	-0.0313	0.2504
miR-34a (78)	0.0303	-0.2428
miR-20a (46)	0.029	-0.2319
miR-218-2 (221)	-0.0252	0.2018
miR-29a (62)	0.0247	-0.1978
miR-25 (55)	0.0233	-0.1861
miR-95 (84)	0.0233	-0.1861
miR-197 (189)	0.0198	-0.1587
miR-135-2 (128)	0.0198	-0.1582
miR-187 (173)	0.0192	-0.1535
miR-196-1 (185)	0.0176	-0.1411
miR-148 (146)	0.0175	-0.1401
miR-191 (177)	0.017	-0.136
miR-21 (47)	0.0169	-0.1351
let-7i (10)	0.0163	-0.1303
miR-198 (190)	0.0145	-0.1161
miR-199a-2 (192)	0.0136	-0.1088
miR-30c (70)	0.0133	-0.1062
miR-17-5p (41)	0.0132	-0.1053
miR-92-2 (82)	0.012	-0.0961
miR-146 (144)	0.0113	-0.0908
miR-181b-1 prec (211)	0.011	-0.0878
miR-32 (75)	0.0109	-0.0873
miR-206 (202)	0.0104	-0.083
miR-184 prec (169)	0.0096	-0.0764
miR-29a prec (63)	-0.0095	0.076
miR-29b-2 (95)	0.0092	-0.0739
miR-149 (147)	-0.0084	0.0676
miR-181b-1 (210)	0.0049	-0.0392
miR-196-1 prec (186)	0.0042	-0.0335
miR-93-1 (83)	0.0039	-0.0312
miR-223 (227)	0.0038	-0.0308
miR-16-1 (38)	0.0028	-0.0226
miR-101-1 prec (92)	0.0015	-0.0123
miR-124a-1 (104)	0.0015	-0.0119
miR-26a-1 (56)	0.0015	-0.0119
miR-214 (212)	0.0013	-0.0105
miR-27a (59)	0.0011	-0.0091
miR-24-1 (53)	-8.00E-04	0.0067
miR-106a (99)	7.00E-04	-0.0057
miR-199a-1 (191)	4.00E-04	-0.0029

T
= 1, 45 miRs selected, misclassification error after cross validation of 0.11. Thirty-nine overexpressed miRs in cancer are indicated by positive cancer scores; six down-regulated miRs are indicated by negative cancer scores.

Table 10. MicroRNAs selected by prediction analysis of microarray (PAM) in stomach (cancer vs. normal tissues)

miRNA (ID)	Stomach cancer score	Stomach normal score
miR-223 (227)	0.1896	-0.1806
miR-21 (47)	0.1872	-0.1783
miR-218-2 (221)	-0.1552	0.1478
miR-103-2 (96)	0.1206	-0.1148
miR-92-2 (82)	0.1142	-0.1088
miR-25 (55)	0.1097	-0.1045
miR-136 (130)	-0.1097	0.1045
miR-191 (177)	0.0946	-0.0901
miR-221 (224)	0.0919	-0.0876
miR-125b-2 (111)	0.0913	-0.0869
miR-103-1 (97)	0.0837	-0.0797
miR-214 (212)	0.0749	-0.0713
miR-222 (225)	0.0749	-0.0713
miR-212 prec (209)	-0.054	0.0514
miR-125b-1 (109)	0.0528	-0.0503
miR-100 (91)	0.0526	-0.0501
miR-107 (100)	0.0388	-0.0369
miR-92-1 (81)	0.0369	-0.0351
miR-96 (86)	-0.0306	0.0291
miR-192 (178)	0.0236	-0.0224
miR-23a (50)	0.022	-0.021
miR-215 (213)	0.0204	-0.0194
miR-7-2 (21)	0.0189	-0.018
miR-138-2 (133)	-0.0185	0.0176
miR-24-1 (52)	0.0151	-0.0144
miR-99b (89)	0.0098	-0.0093
miR-33b (76)	-0.0049	0.0046
miR-24-2 (54)	0.0041	-0.0039

T =
1, 28 miRs selected, misclassification error after cross validation of 0.19. Twenty-two overexpressed miRs in cancer are indicated by positive cancer scores; six down-regulated miRs are indicated by negative cancer scores.

Table 11. Differentially regulated miRs in all six solid cancer types vs. normal tissues (T statistics): Two-class comparison

miRNA	ID	Cancer mean	Normal mean	Test stat	Raw P	Adjusted P
miR-21	47	11.538663	9.648338	7.861136	2.00E-06	2.00E-06
miR-141	137	9.024091	7.905398	6.238014	2.00E-06	2.00E-06
miR-212	208	13.540651	14.33617	-6.57942	2.00E-06	2.00E-06
miR-128a prec	113	12.32588	13.522675	-6.76388	2.00E-06	2.00E-06
miR-138-2	133	11.739557	13.144746	-7.01204	2.00E-06	2.00E-06
miR-218-2	221	11.279787	12.539366	-7.40557	2.00E-06	2.00E-06
miR-23b	51	14.169748	15.949736	-8.37744	2.00E-06	2.00E-06
miR-195	184	10.343991	9.172985	5.763262	2.00E-06	1.00E-05
miR-212 prec	209	12.686966	13.661763	-5.83132	4.00E-06	1.00E-05
miR-29b-2	95	11.27556	9.940731	5.660854	2.00E-06	1.40E-05
miR-199a-1	191	10.032008	8.920183	5.528849	2.00E-06	3.00E-05
miR-9-3	28	11.461922	12.570412	-5.43006	2.00E-06	4.60E-05
miR-128a	114	13.024235	13.856624	-5.35102	6.00E-06	7.20E-05
let-7a-1	1	12.616569	13.455246	-5.35346	2.00E-06	7.20E-05
let-7b	5	13.42636	14.068521	-5.17701	1.00E-05	0.000146
miR-16-2	39	10.460707	9.305895	5.048375	4.00E-06	0.000224
miR-199a-2	192	9.714225	8.759237	4.862553	1.00E-05	0.000494
miR-152 prec	151	11.388676	12.357529	-4.83716	2.00E-06	0.00053
miR-16-1	38	10.443169	9.338182	4.755258	1.00E-05	0.00071
miR-30d	72	13.982017	14.775206	-4.5707	1.20E-05	0.001476
miR-34a	78	10.675566	9.63769	4.467301	2.60E-05	0.00217
miR-17-5p	41	11.567244	10.281468	4.341834	3.80E-05	0.0034
miR-128b	115	10.930395	9.947746	4.304764	3.80E-05	0.003912
miR-20a	46	11.409852	10.19284	4.304678	3.20E-05	0.003912
miR-181b-1 prec	211	9.577504	8.804294	4.285968	4.80E-05	0.004126
miR-132	121	9.599947	8.775966	4.284737	5.60E-05	0.004126
miR-200b	195	9.475221	8.527243	4.221511	4.00E-05	0.0052
let-7a-3	4	10.436089	9.511546	4.08952	0.000104	0.008242
miR-138-1	132	8.299613	9.200253	-4.05204	5.60E-05	0.00931
miR-29c	65	11.291005	10.326912	4.019385	0.000144	0.010312
miR-29a	62	11.381359	10.461075	4.013697	0.00015	0.010398
miR-96	86	11.37218	12.136636	-3.94825	0.000138	0.012962
miR-191	177	13.498207	12.729872	3.817228	0.000158	0.02015
miR-27a	59	10.399338	9.548582	3.715048	0.000344	0.028096
let-7g	15	10.819688	10.01157	3.653239	0.000426	0.033874
miR-9-1	24	10.102819	9.212988	3.651886	0.000388	0.033874
miR-125a	107	10.960998	10.005312	3.651356	0.000452	0.033874
miR-95	84	9.435733	8.751331	3.59406	0.000478	0.039594
miR-155	157	12.505359	13.231221	-3.58369	0.000614	0.040394
miR-199b	194	9.755066	9.082751	3.55934	0.000588	0.04314
miR-24-2	54	12.611696	11.612557	3.518774	0.00087	0.048278
let-7e	11	12.497795	13.055093	-3.51589	0.00054	0.048354
miR-92-1	81	16.081074	16.592426	-3.50446	0.000928	0.049828

Forty-three miRs have an adjusted P value lower than 0.05. Twenty-six miRs are overexpressed and 17 underregulated in breast, colon, lung, pancreas, prostate, and stomach carcinomas when compared with the normal tissues

Table 12. Differentially regulated miRs in six solid cancer types vs. normal tissues (SAM, significance analysis of microarrays)

miRNA	ID	d value	SD	P value	q value	R _fold
miR-21	#47	3.156	0.24	0	0	2.593
miR-23b	#51	-3.117	0.212	0	0	0.443
miR-138-2	#133	-2.514	0.2	0	0	0.402
miR-218-2	#221	-2.383	0.17	0	0	0.384
miR-29b-2	#95	2.246	0.236	0	0	1.868
miR-128a prec	#113	-2.235	0.177	0	0	0.368
miR-195	#184	2.085	0.203	0	0	1.695
miR-141	#137	2.08	0.179	0	0	2.459
miR-199a-1	#191	1.987	0.201	0	0	1.945
miR-9-3	#28	-1.97	0.204	0	0	0.433
miR-16-2	#39	1.966	0.229	0	0	1.788
miR-17-5p	#41	1.964	0.296	0	0	0.725
miR-20a	#46	1.898	0.283	0	0	0.969
miR-16-1	#38	1.87	0.232	0	0	1.447
miR-212 prec	#209	-1.854	0.167	0	0	0.509
miR-34a	#78	1.756	0.232	0	0	1.219
miR-152 prec	#151	-1.734	0.2	0	0	0.46
miR-199a-2	#192	1.721	0.196	0	0	1.838
miR-128b	#115	1.674	0.228	0	0	1.266
miR-212	#208	-1.659	0.121	0	0	0.627
let-7a-1	#1	-1.628	0.157	0	0	0.461
miR-200b	#195	1.626	0.225	0	0	1.432
miR-128a	#114	-1.619	0.156	0	0	0.511
miR-29c	#65	1.611	0.24	0	0	1.225
let-7a-3	#4	1.581	0.226	0	0	1.109
miR-29a	#62	1.565	0.229	0	0	1.706
miR-24-2	#54	1.555	0.284	0	0	0.831
miR-138-1	#132	-1.551	0.222	0	0	0.432
miR-125a	#107	1.541	0.262	0	0	1.164
miR-106a	#99	1.514	0.275	0	0	0.952
miR-132	#121	1.496	0.192	0	0	2.158
miR-30d	#72	-1.491	0.174	0	0	0.424
miR-9-1	#24	1.478	0.244	0	0	0.763
miR-27a	#59	1.448	0.229	0	0	1.174
miR-181b-1 prec	#211	1.435	0.18	0	0	1.525
let-7g	#15	1.394	0.221	0	0	1.072
miR-96	#86	-1.384	0.194	0	0	0.519
miR-191	#177	1.372	0.201	0	0	1.165
miR-93-1	#83	1.363	0.266	0	0	0.775
miR-136	#130	-1.355	0.267	0	0	0.364
miR-205	#201	1.343	0.309	0	0	1.281
miR-185	#170	1.287	0.222	0.001	0.001	0.609
miR-125b-1	#109	1.262	0.283	0.001	0.001	1.215
miR-10a	#30	1.252	0.227	0.001	0.001	1.643
miR-95	#84	1.247	0.19	0.001	0.001	1.509
miR-199b	#194	1.228	0.189	0.001	0.001	1.246
miR-10b	#32	1.219	0.232	0.002	0.001	1.342
let-7i	#10	1.216	0.203	0.002	0.001	1.026
miR-210	#205	1.213	0.237	0.002	0.001	1.088

Thirty-five miRs are overexpressed and 14 are underregulated in breast, colon, lung, pancreas, prostate, and stomach carcinomas (Delta = 0.9, false discovery rate = 0.001).

Table 13. MicroRNAs selected by PAM (prediction analysis of microarray) in six solid cancer types vs. normal tissues

miRNA	ID	Solid cancer score	Normal tissues score
miR-21	47	0.0801	-0.2643
miR-138-2	133	-0.055	0.1815
miR-218-2	221	-0.0535	0.1765
miR-23b	51	-0.0516	0.17
miR-128a prec	113	-0.0498	0.1642
miR-29b-2	95	0.0457	-0.1508
miR-195	184	0.0404	-0.1333
miR-17-5p	41	0.0383	-0.1263
miR-9-3	28	-0.0357	0.1176
miR-212 prec	209	-0.0342	0.1129
miR-20a	46	0.0322	-0.1061
miR-141	137	0.0322	-0.1061
miR-199a-1	191	0.0319	-0.1053
miR-16-2	39	0.0315	-0.1037
miR-152 prec	151	-0.0283	0.0933
miR-16-1	38	0.0277	-0.0913
miR-34a	78	0.0269	-0.0886
miR-212	208	-0.0265	0.0875
let-7a-1	1	-0.0264	0.0872
miR-128a	114	-0.0259	0.0855
miR-128b	115	0.0254	-0.0839
miR-24-2	54	0.0244	-0.0803
miR-29c	65	0.0224	-0.0738
miR-199a-2	192	0.0223	-0.0736
let-7a-3	4	0.0221	-0.073
miR-191	177	0.0188	-0.062
miR-125a	107	0.0186	-0.0613
miR-30d	72	-0.0185	0.061
miR-29a	62	0.0184	-0.0608
miR-106a	99	0.0177	-0.0584
miR-93-1	83	0.0163	-0.0537
miR-200b	195	0.0159	-0.0524
let-7g	15	0.0158	-0.0521
miR-27a	59	0.0157	-0.0518
miR-96	86	-0.0156	0.0514
let-7b	5	-0.0152	0.0501
miR-138-1	132	-0.0151	0.0499
miR-9-1	24	0.0136	-0.0448
miR-181b-1 prec	211	0.0134	-0.0442
miR-155	157	-0.0128	0.0423
miR-132	121	0.0127	-0.0418
miR-136	130	-0.0112	0.037
let-7i	10	0.0103	-0.034
miR-210	205	0.0074	-0.0245
miR-205	201	0.0073	-0.024
miR-185	170	0.0071	-0.0234
miR-24-1	52	0.007	-0.023
miR-199b	194	0.0064	-0.021
miR-125b-1	109	0.006	-0.0199
miR-206 prec	203	-0.005	0.0166
miR-10a	30	0.0045	-0.015
miR-95	84	0.0045	-0.0149
let-7e	11	-0.0039	0.013
miR-124a-3	106	-0.0028	0.0091
miR-10b	32	0.002	-0.0066
miR-185 prec	171	-0.0014	0.0047
miR-92-1	81	-2.00E-04	5.00E-04

T
= 1.5 and misclassification error = 0.176. Thirty-six overexpressed miRs in cancer are indicated by positive cancer scores; 21 down-regulated miRs are indicated by negative cancer scores.

Table 14. Oncogenes and tumor suppressor genes predicted by TargetScanS as targets of microRNAs from the described microRNA cancer subset*

miRNA gene	Gene name	Gene description
miR-26a, miR-146	ABL2	v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)
miR-107	AF5q31	ALL1 fused gene from 5q31
miR-20, miR-125b	AKT3	v-akt murine thymoma viral oncogene homolog 3
miR-26a, miR-155 miR-125b	APC	adenomatosis polyposis coli
miR-26a, miR-218	ARHGEF12	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)
miR-107, miR-221	ARNT	aryl hydrocarbon receptor nuclear translocator
miR-192	ATF1	activating transcription factor 1
miR-26a	ATM	Ataxia telangiectasia mutated (includes complementation groups A, C and D)
miR-24	AXL	AXL receptor tyrosine kinase
miR-26a, miR-107, miR-146, miR-155 miR-138, miR-92	BCL11A	B-cell CLL/lymphoma 11A
miR-20	BCL11B	B-cell CLL/lymphoma 11B (CTIP2)
miR-21	BCL2	B-cell CLL/lymphoma 2
miR-26a, miR-26a miR-20,	BCL6	B-cell CLL/lymphoma 6 (zinc finger protein 51)
miR-92	BCL9	B-cell CLL/lymphoma 9
miR-26a, miR-223 miR-221, miR-125b	CBFB	core-binding factor, beta subunit
miR-218	CCDC6	coiled-coil domain containing 6
miR-20	CCND1	cyclin D1 (PRAD1: parathyroid adenomatosis 1)
miR-26a, miR-20	CCND2	cyclin D2
miR-26a, miR-107, miR-92	CDK6	cyclin-dependent kinase 6
miR-20	CDKN1A	cyclin-dependent kinase inhibitor 1A (p21, Cip1)
miR-221, miR-92	CDKN1C	cyclin-dependent kinase inhibitor 1C (p57, Kip2)
miR-24	CDX2	caudal type homeo box transcription factor 2
miR-92	CEBPA	CCAAT/enhancer binding protein (C/EBP), alpha
miR-26a	CLTC	clathrin, heavy polypeptide (Hc)
miR-218	COL1A1	collagen, type I, alpha 1
miR-26a	CREBBP	CREB binding protein (CBP)
miR-20	CRK	v-crk avian sarcoma virus CT10 oncogene homolog
miR-20	CSF1	colony stimulating factor 1 (macrophage)
miR-221, miR-192	DDX6	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)
miR-138	DEK	DEK oncogene (DNA binding)
miR-20	E2F1	E2F transcription factor 1
miR-20	ELK3	ELK3, ETS-domain protein (SRF accessory protein 2)
miR-24	ELL	ELL gene (11-19 lysine-rich leukemia gene)
miR-26a, miR-138	ERBB4	v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4
miR-221, miR-155, miR-125b	ETS1	v-ets avian erythroblastosis virus E26 oncogene homolog 1
miR-20	ETV1	ets variant gene 1
miR-125b	ETV6	ets variant gene 6 (TEL oncogene)
miR-223	FAT	FAT tumor suppressor (Drosophila) homolog
miR-223, miR-125b, miR-218	FGFR2	fibroblast growth factor receptor 2
miR-92	FLI1	Friend leukemia virus integration 1
miR-24, miR-20	FLT1	fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)
miR-221	FOS	v-fos FBJ murine osteosarcoma viral oncogene homolog
miR-92	FOXG1B	forkhead box G1B
miR-223	FOXO3A	forkhead box O3A
miR-125b	GOLGA5	golgi autoantigen, golgin subfamily a, 5 (PTC5)
miR-138	GPHN	gephyrin (GPH)
miR-107, miR-223, miR-20, miR-218	HLF	hepatic leukemia factor
miR-26a, miR-107	HMGA1	high mobility group AT-hook 1
miR-20	HOXA13	homeo box A13
miR-92	HOXA9	homeo box A9
miR-125b	IRF4	interferon regulatory factor 4
miR-146, miR-20, miR-138	JAZF1	juxtaposed with another zinc finger gene 1
miR-92	JUN	v-jun avian sarcoma virus 17 oncogene homolog
miR-155	KRAS	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog
miR-218	LASP1	LIM and SH3 protein 1
miR-218	LHFP	lipoma HMGIC fusion partner
miR-125b, miR-218	LIFR	leukemia inhibitory factor receptor
miR-223	LMO2	LIM domain only 2 (rhombotin-like 1) (RBTN2)
miR-223, miR-155, miR-125b, miR-92	MAF	v-maf musculoaponeurotic fibrosarcoma (avian) oncogene homolog
miR-92	MAP2K4	mitogen-activated protein kinase kinase 4
miR-146, miR-20	MAP3K8	mitogen-activated protein kinase kinase kinase 8
miR-125b	MAX	MAX protein
miR-218	MCC	mutated in colorectal cancers
miR-24	MEN1	multiple endocrine neoplasia I
miR-138	MLLT6	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)
miR-192	MSN	moesin
miR-24	MYB	v-myb avian myeloblastosis viral oncogene homolog
miR-107, miR-223, miR-146, miR-221, miR-155, miR-218	MYBL1	v-myb avian myeloblastosis viral oncogene homolog-like 1
miR-107, miR-20	MYCN	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived
miR-107, miR-92	MYH9	myosin, heavy polypeptide 9, non-muscle
miR-24	MYST4	MYST histone acetyltransferase (monocytic leukemia) 4 (MORF)
miR-20	NBL1	neuroblastoma, suppression of tumorigenicity 1
miR-125b	NIN	ninein (GSK3B interacting protein)
miR-26a, miR-107	NKTR	natural killer-tumor recognition sequence
miR-92	NOTCH1	Notch homolog 1, translocation-associated (Drosophila) (TAN1)
miR-24	NTRK3	neurotrophic tyrosine kinase, receptor, type 3
miR-125b	PCSK7	proprotein convertase subtilisin/kexin type 7
miR-24, miR-146	PER1	period homolog 1 (Drosophila)
miR-146, miR-125b, miR-138,	PHOX2B	paired-like homeobox 2b
miR-155	PICALM	phosphatidylinositol binding clathrin assembly protein (CALM)
miR-24, miR-26a	PIM1	pim-1 oncogene
miR-24, miR-26a, miR-21, miR-107, miR-20, miR-155	PLAG1	pleiomorphic adenoma gene 1
miR-218	RAB8A	RAB8A, member RAS oncogene family
miR-24, miR-221	RALA	v-ral simian leukemia viral oncogene homolog A (ras related)
miR-138	RARA	retinoic acid receptor, alpha
miR-20, miR-106,miR-192	RB1	retinoblastoma 1 (including osteosarcoma)
miR-20,	RBL1	retinoblastoma-like 1 (p107)
miR-20	RBL2	retinoblastoma-like 2 (p130)
miR-155, miR-138	REL	v-rel avian reticuloendotheliosis viral oncogene homolog
miR-20, miR-138	RHOC	ras homolog gene family, member C
miR-20, miR-192	RUNX1	runt-related transcription factor 1 (AML1)
miR-107, miR-223	SEPT6	septin 6
miR-146, miR-20, miR-125b	SET	SET translocation
miR-21, miR-20, miR-155, miR-218	SKI	v-ski avian sarcoma viral oncogene homolog
miR-26a, miR-146	SMAD4	SMAD, mothers against DPP homolog 4 (Drosophila)
miR-155	SPI1	spleen focus forming virus (SFFV) proviral integration oncogene spi1
miR-125b	SS18	synovial sarcoma translocation, chromosome 18
miR-107, miR-155	SUFU	suppressor of fused homolog (Drosophila)
miR-92	TAF15	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa
miR-26a, miR-221, miR-138	TCF12	transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)
miR-21, miR-20	TGFBR2	transforming growth factor, beta receptor II (70-80kD)
miR-24, miR-26a, miR-92	TOP1	topoisomerase (DNA) I
miR-138	TPM4	tropomyosin 4
miR-20	TRIP11	thyroid hormone receptor interactor 11
miR-92	TSC1	Tuberous sclerosis 1
miR-20	TSG101	Tumor susceptibility gene 101
miR-20	TUSC2	Tumor suppressor candidate 2
miR-24	VAV1	vav 1 oncogene
miR-125b	VAV2	vav 2 oncogene
miR-107	WHSC1	Wolf-Hirschhorn syndrome candidate 1(MMSET)
miR-138	WHSC1L1	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)
miR-26a	WNT5A	wingless-type MMTV integration site family, member 5A
miR-26a, miR-20, miR-125b	YES1	v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1
miR-107, miR-221	ZNF198	zinc finger protein 198
miR-218	ZNFN1A1	zinc finger protein, subfamily 1A, 1 (Ikaros)

*Known cancer genes list (tumor suppressors and oncogenes) was as identified in the Cancer Gene Census at www.sanger.ac.uk/genetics/CGP/Census/ or reported by OMIM at www.ncbi.nlm.nih.gov.