1
Table S1. Variation in the expression pattern of abundantly expressed miRNAs across
2
different samples.
3
Samples
Patient 1-tumor
Patient 1-normal
Patient 2-tumor
Patient 2-normal
Patient 3-tumor
Patient 3-normal
Patient 4-tumor
Patient 4-normal
Patient 5-tumor
Patient 5-normal
Patient 6-tumor
Patient 6-normal
Patient 7-tumor
Patient 7-normal
Normal-serum 1 (10 mixed)
Normal-serum 2 (10 mixed)
Normal-serum 3 (10 mixed)
Tumor-serum 1 (10 mixed)
Tumor-serum 2 (10 mixed)
Abundantly expressed miRNAs
34
37
39
47
47
35
43
43
48
44
50
45
46
50
54
47
52
56
55
All the expressed miRNAs
626
395
656
234
736
231
354
524
301
274
206
187
192
330
490
206
263
331
341
4
Relative expression levels of these involved abundantly expressed miRNAs are at least 0.30% in the sample.
5
6
Moreover, numbers of all the expressed miRNAs are also listed here.
7
Table S2. Aberrantly expressed miRNA species in breast cancer tissues based on their
8
adjacent normal tissues in the 7 patients.
9
Sample (patient)
Up (13)
P
1
Aberrantly expressed miRNAs
miR-223, miR-761, miR-222, miR-21, miR-23b, miR-29c, miR-29b, miR-192, miR-23a,
miR-29a, miR-125b, miR-129-3p, miR-142-5p
miR-1287, miR-188-5p, miR-455-5p, miR-1273, miR-767-3p, miR-1914, miR-3074,
Down (18)
miR-1303, miR-525-5p, miR-3184, miR-3065-5p, miR-551b*, miR-3183, miR-1972,
miR-500, miR-1273d, miR-103b, let-7b
miR-130a, miR-196a, miR-425, miR-29b, miR-532-5p, miR-1260b, miR-191, miR-187,
Up (19)
miR-708, miR-342-5p, miR-590-5p, miR-451, miR-489, miR-130b, miR-1260, miR-223,
miR-342-3p, miR-150, miR-192
P
miR-4305, miR-619, miR-126*, miR-27a, miR-126, miR-20a, let-7e, miR-18a, miR-19b,
2
Down (29)
miR-30a, miR-324-5p, miR-21, miR-218, miR-30d, miR-320a, miR-181a, miR-100,
miR-146a, miR-10a, miR-93, miR-23a, miR-26a, miR-301a, miR-99a, miR-34a,
miR-92a, let-7a, miR-17, miR-23b
P
3
Up (15)
Down (4)
miR-130b, miR-342-3p, miR-126, miR-99b, miR-590-5p, miR-200c, miR-99a,
miR-1260, miR-145, miR-192, miR-140-3p, miR-24, miR-223, miR-150, miR-451
miR-483-5p, miR-454, miR-675, miR-103b
1
P
4
miR-25, miR-22, miR-451, miR-141, miR-200c, miR-193a-5p, miR-574-5p, miR-205,
Up (13)
miR-146b-5p, miR-146a, miR-339-5p, let-7i, miR-210
Down (13)
let-7d, miR-26b, miR-135b, miR-26a, let-7a, miR-361-5p, let-7f, miR-148a, miR-214,
miR-15b, miR-29b, miR-29c, miR-150
P
Up (5)
miR-22, let-7f, miR-1308, miR-15b, miR-124
5
Down (3)
miR-324-5p, miR-135a, let-7b
P
Up (6)
miR-145, miR-375, miR-146a, miR-124, miR-146b-5p, miR-200b
6
Down (3)
miR-1308, miR-30a, miR-451
P
Up (4)
miR-182, miR-103, miR-93, miR-17
7
Down (8)
miR-10b, let-7i, miR-21, miR-22, miR-150, miR-451, miR-125b, miR-99a
10
11
Table S3. Aberrantly expressed miRNAs in breast tissues based on mixed data of 7 paired
12
tumor and adjacent normal tissue samples.
13
Different method
Aberrantly expressed miRNAs
miR-221, miR-19b, miR-451, miR-126, miR-140-3p, let-7i, miR-223, miR-342-5p,
Total
Up (17)
miR-1308, miR-191, miR-130a, miR-130b, miR-210, miR-342-3p, miR-708,
miR-192, miR-1260
(counts)
Down (8)
miR-361-5p, miR-26b, miR-135b, miR-26a, miR-214, miR-15b, miR-29c, miR-155
Total
Up (5)
miR-130b, miR-223, miR-210, miR-342-3p, miR-192
(percent)
Down (4)
miR-1287, miR-188-5p, miR-103b, miR-126*
14
The final expression data are mixed based on original sequence counts (counts) and relative expression levels
15
(percent), respectively. Due to involved in variety of total sequence counts between different samples, the final
16
17
expression data based on relative expression levels are more reasonable than other method.
18
Table S4. Functional enrichment pathway analysis of experimentally validated target genes
19
of aberrantly expressed miRNAs in Table 2.
20
Count
Enrichment
(no.)
P-value
Chronic myeloid leukemia
9
1.79E-16
MAPK signaling pathway
9
2.61E-11
Bladder cancer
8
1.80E-16
8
8.56E-14
Prostate cancer
8
9.40E-14
Pancreatic cancer
8
1.99E-14
Colorectal cancer
7
6.76E-12
Pathway
TGF-beta signaling
pathway
Target Genes
ACVR1C;CDKN1A;E2F1;E2F3;KRAS;MYC;NRAS;
SMAD4;TGFBR2
ACVR1C;BDNF;KRAS;MAPK9;MYC;NRAS;PTPN7;
STMN1;TGFBR2
CDKN1A;E2F1;E2F3;KRAS;MYC;NRAS;THBS1;
VEGFA
ACVR1C;BMP7;BMPR2;MYC;RBL2;SMAD4;
TGFBR2;THBS1
BCL2;CDK2;CDKN1A;E2F1;E2F3;KRAS;NRAS;PTEN
ACVR1C;E2F1;E2F3;KRAS;MAPK9;SMAD4;
TGFBR2;VEGFA
ACVR1C;BCL2;KRAS;MAPK9;MYC;SMAD4;TGFBR2
2
Cell cycle
7
8.11E-11
CCND2;CDK2;CDKN1A;E2F1;E2F3;RBL2;SMAD4
Focal adhesion
7
3.66E-09
BCL2;CCND2;PAK3;MAPK9;PTEN;THBS1;VEGFA
Glioma
6
1.25E-10
CDKN1A;E2F1;E2F3;KRAS;NRAS;PTEN
Melanoma
6
2.15E-10
CDKN1A;E2F1;E2F3;KRAS;NRAS;PTEN
Small cell lung cancer
6
6.97E-10
BCL2;CDK2;E2F1;E2F3;MYC;PTEN
ErbB signaling pathway
6
7.48E-10
CDKN1A;PAK3;KRAS;MAPK9;MYC;NRAS
p53 signaling pathway
5
1.65E-08
CCND2;CDK2;CDKN1A;PTEN;THBS1
5
1.23E-05
BMP7;BMPR2;IL6;TGFBR2;VEGFA
Thyroid cancer
4
3.43E-08
KRAS;MYC;NRAS;PPARG
Endometrial cancer
4
3.84E-07
KRAS;MYC;NRAS;PTEN
Non-small cell lung cancer
4
4.48E-07
E2F1;E2F3;KRAS;NRAS
Acute myeloid leukemia
4
6.42E-07
KRAS;MYC;NRAS;PIM1
Renal cell carcinoma
4
1.36E-06
PAK3;KRAS;NRAS;VEGFA
4
7.52E-06
PAK3;KRAS;MAPK9;NRAS
Axon guidance
4
1.51E-05
PAK3;GNAI2;KRAS;NRAS
Tight junction
4
1.80E-05
GNAI2;KRAS;NRAS;PTEN
Wnt signaling pathway
4
2.79E-05
CCND2;MAPK9;MYC;SMAD4
4
3.01E-05
CCND2;IL6;MYC;PIM1
Cytokine-cytokine receptor
interaction
T cell receptor signaling
pathway
Jak-STAT signaling
pathway
21
22
Here, we only listed important pathways that are involved in at least 4 target mRNAs. These mRNAs are regulated
23
24
by at least 2 aberrantly expressed miRNAs in breast cancers.
25
Table S5. Functional enrichment pathway analysis of target genes of aberrantly expressed
26
let-7 and miR-30 gene families, and miR-30b gene cluster.
27
Count
Enrichment
(no.)
P-value
p53 signaling pathway
5
2.81E-07
CDK6;SERPINE1;THBS1;TNFRSF10B;TP53
Melanoma
5
3.25E-07
CDK6;E2F1;MET;RB1;TP53
Small cell lung cancer
5
8.49E-07
CDK6;E2F1;ITGA2;RB1;TP53
Axon guidance
5
6.52E-06
CXCL12;GNAI2;MET;PPP3CA;PPP3R1
Wnt signaling pathway
5
1.39E-05
JUN;PPP3CA;PPP3R1;TP53;WNT5A
MAPK signaling pathway
5
2.30E-04
JUN;PPP3CA;PPP3R1;STMN1;TP53
Bladder cancer
4
1.54E-06
E2F1;RB1;THBS1;TP53
Non-small cell lung cancer
4
4.27E-06
CDK6;E2F1;RB1;TP53
Glioma
4
8.99E-06
CDK6;E2F1;RB1;TP53
Pancreatic cancer
4
1.43E-05
CDK6;E2F1;RB1;TP53
Chronic myeloid leukemia
4
1.59E-05
CDK6;E2F1;RB1;TP53
Apoptosis
4
3.13E-05
PPP3CA;PPP3R1;TNFRSF10B;TP53
Pathway
Target Genes
3
Cell cycle
4
9.72E-05
CDK6;E2F1;RB1;TP53
Focal adhesion
4
7.68E-04
ITGA2;JUN;MET;THBS1
4
2.00E-03
CXCL12;IL6R;MET;TNFRSF10B
Cytokine-cytokine receptor
interaction
28
29
30
31
Here, we only list important pathways that involve at least 4 target mRNAs.
Table S6. Several aberrantly expressed miRNAs in breast cancer according to published
papers.
32
miRNA
Deregulation
Validated method
References
miR-145
down
microarray and Northern blot
[13]
miR-125b
down
microarray and Northern blot
[13]
miR-21
up
microarray and Northern blot
[13]
miR-10b
up
Real-time PCR
[14]
miR-9
up
Real-time PCR
[14]
miR-31
down
Real-time PCR
[15]
miR-221
up
Real-time PCR
[16]
miR-222
up
Real-time PCR
[16]
miR-181
up
Real-time PCR
[16]
miR-342
down
Real-time PCR
[16]
miR-489
down
Real-time PCR
[16]
miR-200c
down
Real-time PCR
[17]
miR-27a
up
Real-time PCR
[18]
miR-206
down
Real-time PCR
[19]
miR-146
down
Real-time PCR
[20]
33
34
4