In this work, we obtained confident miRNA-target pairs by combining differentially expressed miRNAs and mRNAs elucidated from expression profiles and popular target prediction databases. By incorporating known protein interaction data in HPRD and confident miRNA-target pairs, breast cancer specific miRNA-regulated networks were constructed. After network construction, putative functions of the miRNA-regulated networks were discovered by GO enrichment analysis. From the result, we found previously known miRNAs which were enriched with cancer-related terms, such as “apoptosis” and “cell proliferation”. Novel breast cancer related miRNAs and putative functions of their PINs were also discovered in our work. We also validated some of our results by ROC curve analysis, survival analysis (GOBO), and literature search. This work may contribute to further research of breast cancer and related miRNAs, since some novel miRNAs associated with breast cancer were found.
Furthermore, it is also possible to apply the method used in this work to other cancers for novel cancer-associated miRNA discovery and functional elucidation.
FIGURES
Figure 1. Pipeline for miRNA-regulated PINs construction and functional analysis.
Green: external dataset; cyan: external database; blue: dataset generated in the analysis
steps; orange: analyzing steps which do the calculations or preprocessing.Figure 2. Definition of GO level in this work.
GO level was defined as the minimum distance between the term and its root node.
Thus, GO level of GO term Y and term X is 1; GO level of GO term is Z; GO level of GO term A is also 2, since 2 is the minimum distance of the 2 possible paths to its root node.
Figure 3. Schematic figure describing activity analysis.
Red edge stands for co-expressed PPI. A: Co-expression means that expression of two
interacting gene are positively correlated. B: When the co-expressed interactions are enriched in a network (right part), we define it to be activated.A
B
Figure 4. Distribution of miRNA dataset GSE29173.
Each bar represents data distribution of a single sample. A: Distribution, presented in boxplot, of the original dataset. B: Distribution of the dataset after normalization steps.
A
B
Figure 5. Distribution of gene expression dataset GSE29174.
Each bar represents data distribution of a single sample. A: Distribution, presented in boxplot, of the original dataset. B: Distribution of the dataset after normalization steps.
Figure 6. miRNA-regulated PIN (hsa-let-7c).
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 7. miRNA-regulated PIN. (hsa-miR-21-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 8. miRNA-regulate PIN. (hsa-miR-22-3p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 9. miRNA-regulated PINs. (hsa-miR-31-5p and hsa-miR-99a-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 10. miRNA-regulated PINs. (hsa-miR-100-5p and hsa-miR-139-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 11. miRNA-regulated PIN. (hsa-204-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 12. miRNA-regulated PINs. (hsa-miR-214-3p, hsa-miR-215, and hsa-miR-122-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 13. miRNA-regulated PIN. (hsa-miR-125b-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 14. miRNA-regulated PIN. (hsa-miR-145-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 15. miRNA-regulated PIN. (hsa-miR-125a-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 16. miRNA-regulated PINs. (hsa-miR-383 and hsa-miR-193b-3p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 17. miRNA-regulated PIN. (hsa-miR-497-5p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.Figure 18. miRNA-regulated PIN. (hsa-miR-520d-3p)
Red: miRNA; green: direct target of the miRNA; blue: proteins interacting with direct
target of the miRNA.A
B
Figure 19. Distribution of Pearson correlation coefficient of gene pairs in microarray data.
Here, PCC is the expression correlation of two genes. In normal sample, from when PCC > 0.4~0.5, the proportion of PPIPaired is greater than AllPaired. In tumor samples, from when PCC > 0.1~0.2, the proportion of PPIPaired is greater than AllPaired. A:
Distribution of PCCs calculated by normal samples. B: Distribution of PCCs calculated by tumor samples. AllPaired: Distribution of PCCs of gene pairs formed by any two genes in the gene microarray. PPIPaired: Distribution of PCCs of HPRD PPIs.
A. hsa-let-7c. MIMAT0000064. ***
B. hsa-miR-21-5p. MIMAT0000076. ***
Figure 20. ROC curves and expression distribution of miRNAs.
Expression value from NTUH miRNA dataset was used for validating our results. Solid
line: actual prediction performance of the miRNA as diagnostic marker; dashed line:
AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***: p-value <
0.001.
C. hsa-miR-22-3p. MIMAT0000077.
D. hsa-miR-31-5p. MIMAT0000089. ***
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
E. hsa-miR-99a-5p. MIMAT0000097. ***
F. hsa-miR-100-5p. MIMAT0000098. ***
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
G. hsa-miR-139-5p. MIMAT0000250. ***
H. hsa-miR-204-5p. MIMAT0000265. ***
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
I. hsa-miR-214-3p. MIMAT0000271. *
J. hsa-miR-215. MIMAT0000272.
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
K. hsa-miR-122-5p. MIMAT0000421.
L. hsa-miR-125b-5p. MIMAT0000423. ***
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
M. hsa-miR-145-5p. MIMAT0000437. ***
N. hsa-miR-125a-5p. MIMAT0000443.
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
O. hsa-miR-383. MIMAT0000738.
P. hsa-miR-193b-3p. MIMAT0002819.
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
Q. hsa-miR-497-5p. MIMAT0002820. ***
R. hsa-miR-520d-3p. MIMAT0002856.
Figure 20. ROC curves and expression distribution of miRNAs. (continue)
Solid line: actual prediction performance of the miRNA as diagnostic marker; dashed line: AUC = 0.5 (no predictive power). *: p-value < 0.05; **: p-value < 0.01; ***:
p-value < 0.001.
MIMAT0000064 (hsa-let-7c) GO:0015630, Microtubule cytoskeleton
MIMAT0000064 (hsa-let-7c)
GO:0043069, Negative regulation of programmed cell death
MIMAT0000064 (hsa-let-7c)
GO:0060548, Negative regulation of cell death
MIMAT0000089 (hsa-miR-31-5p) GO:0006917, Induction of apoptosis
Figure 21 GOBO Kaplan-Meier survival curve of selected gene set with significant clinical outcome.
The gene set was formed by selecting genes annotated with designated GO term in the miRNA-regulated PIN. Full GOBO Kaplan-Meier survival p-value were calculated and listed in Table 9. *: p < 0.05; **: p < 0.01; ***: p < 0.001.
MIMAT0000089 (hsa-miR-31-5p)
GO:0012502, Induction of programmed cell death
MIMAT0000423 (hsa-miR-125b-5p) GO:0015630, Microtubule cytoskeleton
MIMAT0000423 (hsa-miR-125b-5p)
GO:0050678, Regulation of epithelial cell proliferation
MIMAT0000443 (hsa-miR-125a-5p) GO:0015630, Microtubule cytoskeleton
Figure 21 GOBO Kaplan-Meier survival curve of selected gene set (continue)
*: p < 0.05; **: p < 0.01; ***: p < 0.001.
MIMAT0000443 (hsa-miR-125a-5p)
GO:0050678, Regulation of epithelial cell proliferation
MIMAT0002820 (hsa-miR-497-5p)
GO:0007179, Transforming growth factor beta receptor signaling pathway
MIMAT0002856 (hsa-miR-520d-3p) GO:0015630, Microtubule cytoskeleton
MIMAT0002856 (hsa-miR-520d-3p)
GO:0048011, Nerve growth factor receptor signaling pathway
Figure 21 GOBO Kaplan-Meier survival curve of selected gene set (continue)
*: p < 0.05; **: p < 0.01; ***: p < 0.001.
MIMAT0002856 (hsa-miR-520d-3p)
GO:0051988, Regulation of attachment of spindle microtubules to kinetochore
Figure 21 GOBO Kaplan-Meier survival curve of selected gene set (continue)
*: p < 0.05; **: p < 0.01; ***: p < 0.001.
TABLES
Table 1. Significantly differentially expressed miRNAs found in dataset GSE29173.
There are 89 down-regulated miRNAs and 1 up-regulated miRNA in this list. Q-value reported by SAM were 0 for all miRNAs in this list.
miRBase Accession miRNA Name Fold Change miRBase Accession miRNA Name Fold Change MIMAT0004761 hsa-miR-483-5p 0.01 MIMAT0000077 hsa-miR-22-3p 0.21 MIMAT0004552 hsa-miR-139-3p 0.01 MIMAT0000089 hsa-miR-31-5p 0.21 MIMAT0000738 hsa-miR-383 0.02 MIMAT0004612 hsa-miR-186-3p 0.21 MIMAT0002856 hsa-miR-520d-3p 0.02 MIMAT0004592 hsa-miR-125b-1-3p 0.22 MIMAT0002811 hsa-miR-202-3p 0.03 MIMAT0001639 hsa-miR-409-3p 0.22 MIMAT0002177 hsa-miR-486-5p 0.04 MIMAT0015032 hsa-miR-3158-3p 0.22 MIMAT0022721 hsa-miR-1247-3p 0.05 MIMAT0004496 hsa-miR-23a-5p 0.22 MIMAT0002175 hsa-miR-485-5p 0.06 MIMAT0000690 hsa-miR-296-5p 0.22 MIMAT0000265 hsa-miR-204-5p 0.07 MIMAT0000731 hsa-miR-378a-5p 0.23 MIMAT0000752 hsa-miR-328 0.07 MIMAT0000448 hsa-miR-136-5p 0.23 MIMAT0000421 hsa-miR-122-5p 0.07 MIMAT0004796 hsa-miR-576-3p 0.23
MIMAT0000447 hsa-miR-134 0.08 MIMAT0010133 hsa-miR-2110 0.23
MIMAT0000722 hsa-miR-370 0.09 MIMAT0004951 hsa-miR-887 0.23
MIMAT0004513 hsa-miR-101-5p 0.09 MIMAT0003239 hsa-miR-574-3p 0.25 MIMAT0000446 hsa-miR-127-3p 0.10 MIMAT0005901 hsa-miR-1249 0.25 MIMAT0000097 hsa-miR-99a-5p 0.10 MIMAT0000510 hsa-miR-320a 0.26 MIMAT0004566 hsa-miR-218-2-3p 0.10 MIMAT0002172 hsa-miR-376b 0.26 MIMAT0000729 hsa-miR-376a-3p 0.11 MIMAT0000250 hsa-miR-139-5p 0.27 MIMAT0009197 hsa-miR-205-3p 0.11 MIMAT0005825 hsa-miR-1180 0.27 MIMAT0004615 hsa-miR-195-3p 0.11 MIMAT0000437 hsa-miR-145-5p 0.28 MIMAT0005899 hsa-miR-1247-5p 0.11 MIMAT0004601 hsa-miR-145-3p 0.28 MIMAT0000720 hsa-miR-376c 0.12 MIMAT0003322 hsa-miR-652-3p 0.28 MIMAT0000762 hsa-miR-324-3p 0.12 MIMAT0000756 hsa-miR-326 0.28 MIMAT0004679 hsa-miR-296-3p 0.12 MIMAT0000098 hsa-miR-100-5p 0.29 MIMAT0004614 hsa-miR-193a-5p 0.12 MIMAT0003296 hsa-miR-627 0.29 MIMAT0003880 hsa-miR-671-5p 0.12 MIMAT0002820 hsa-miR-497-5p 0.31 MIMAT0004795 hsa-miR-574-5p 0.12 MIMAT0004507 hsa-miR-92a-1-5p 0.31 MIMAT0004599 hsa-miR-143-5p 0.13 MIMAT0000271 hsa-miR-214-3p 0.32 MIMAT0000423 hsa-miR-125b-5p 0.13 MIMAT0004702 hsa-miR-339-3p 0.33 MIMAT0004957 hsa-miR-760 0.13 MIMAT0004611 hsa-miR-185-3p 0.33
MIMAT0004911 hsa-miR-874 0.14 MIMAT0000064 hsa-let-7c 0.34
MIMAT0004603 hsa-miR-125b-2-3p 0.15 MIMAT0004673 hsa-miR-29c-5p 0.35 MIMAT0004952 hsa-miR-665 0.15 MIMAT0000733 hsa-miR-379-5p 0.35 MIMAT0018205 hsa-miR-3928 0.15 MIMAT0004594 hsa-miR-132-5p 0.35 MIMAT0004767 hsa-miR-193b-5p 0.15 MIMAT0000765 hsa-miR-335-5p 0.35 MIMAT0002861 hsa-miR-518e-3p 0.15 MIMAT0002819 hsa-miR-193b-3p 0.36 MIMAT0004604 hsa-miR-127-5p 0.16 MIMAT0000088 hsa-miR-30a-3p 0.36 MIMAT0002807 hsa-miR-491-5p 0.16 MIMAT0005951 hsa-miR-1307-3p 0.36 MIMAT0004689 hsa-miR-377-5p 0.16 MIMAT0004597 hsa-miR-140-3p 0.37 MIMAT0004762 hsa-miR-486-3p 0.16 MIMAT0004556 hsa-miR-10b-3p 0.37 MIMAT0000732 hsa-miR-378a-3p 0.17 MIMAT0000272 hsa-miR-215 0.37 MIMAT0017981 hsa-miR-3605-5p 0.18 MIMAT0004511 hsa-miR-99a-3p 0.37 MIMAT0004605 hsa-miR-129-2-3p 0.19 MIMAT0000443 hsa-miR-125a-5p 0.38 MIMAT0006789 hsa-miR-1468 0.20 MIMAT0004482 hsa-let-7b-3p 0.38 MIMAT0000737 hsa-miR-382-5p 0.21 MIMAT0000076 hsa-miR-21-5p 6.58
Table 2. Down-regulated genes found in dataset GSE29174.
There are 726 down-regulated genes in this list. Q-values reported by SAM were 0 for all genes in this list.
NCBI gene ID Gene Symbol Fold Change NCBI gene ID Gene Symbol Fold Change
Table 2. Down-regulated genes found in dataset GSE29174. (continue)
Table 2. Down-regulated genes found in dataset GSE29174. (continue)
Table 2. Down-regulated genes found in dataset GSE29174. (continue)
Table 2. Down-regulated genes found in dataset GSE29174. (continue)
Table 2. Down-regulated genes found in dataset GSE29174. (continue)
Table 2. Down-regulated genes found in dataset GSE29174. (continue)
Table 3. Up-regulated genes found in dataset GSE29174.
Table 3. Up-regulated genes found in dataset GSE29174. (continue)
Table 3. Up-regulated genes found in dataset GSE29174. (continue)
Table 3. Up-regulated genes found in dataset GSE29174. (continue)
Table 3. Up-regulated genes found in dataset GSE29174. (continue)
NCBI gene ID Gene Symbol Fold Change NCBI gene ID Gene Symbol Fold Change
26057 ANKRD17 1.95 7332 UBE2L3 1.92
128061 C1orf131 1.95 3336 HSPE1 1.92
64090 GAL3ST2 1.94 54800 KLHL24 1.92
130507 UBR3 1.93 2290 FOXG1 1.91
2298 FOXD4 1.93 50848 F11R 1.91
123169 LEO1 1.93 10627 MYL12A 1.91
57187 THOC2 1.93 5074 PAWR 1.91
148789 B3GALNT2 1.93 6476 SI 1.91
58508 MLL3 1.92 1009 CDH11 1.90
5701 PSMC2 1.92 29066 ZC3H7A 1.90
148066 ZNRF4 1.92 51319 RSRC1 1.90
6670 SP3 1.92
Table 4. Raw data count of each prediction database.
Prediction database used in this work and their corresponding unique prediction count were listed. Prediction count: a unique miRNA-target pair was counted as one prediction.
Target prediction database Prediction count
TargetScan 6.0 4305160
miRanda (Aug. 2010) 7333699
picTar (5sp) 56058
Table 5. Summary of constructed miRNA-regulated networks.
L0 gene: genes connected directly to the miRNA (i.e. direct target of miRNA); L1 gene:
genes not connected directly to the miRNA.
miRBase Accession miR name Total gene count L0 count L1 count
MIMAT0002819 hsa-miR-193b-3p 16 1 15
MIMAT0000250 hsa-miR-139-5p 28 10 18
MIMAT0000437 hsa-miR-145-5p 86 22 64
MIMAT0000423 hsa-miR-125b-5p 211 16 195
MIMAT0000443 hsa-miR-125a-5p 206 14 192
MIMAT0000097 hsa-miR-99a-5p 14 1 13
MIMAT0000265 hsa-miR-204-5p 64 18 46
MIMAT0000076 hsa-miR-21-5p 91 16 75
MIMAT0000064 hsa-let-7c 96 20 76
MIMAT0000421 hsa-miR-122-5p 5 3 2
MIMAT0000098 hsa-miR-100-5p 14 1 13
MIMAT0000272 hsa-miR-215 3 3 0
MIMAT0000271 hsa-miR-214-3p 14 8 6
MIMAT0000738 hsa-miR-383 34 3 31
MIMAT0002856 hsa-miR-520d-3p 146 23 123
MIMAT0000077 hsa-miR-22-3p 46 11 35
MIMAT0002820 hsa-miR-497-5p 267 32 235
MIMAT0000089 hsa-miR-31-5p 34 3 31
Table 6. Specific enriched GO terms of each miRNA-regulated PINs.
Genes annotated with the specific GO term in the PIN were also listed in this table. Adj. p-value: multiple-test adjusted p-value calculated by the method described in the work of Benjamini and Yekutieli [42].
MIMAT0002856(hsa-miR-520d-3p)
GO term Genes Adj. p-value
GO:0007169, Transmembrane receptor protein tyrosine kinase signaling pathway
SH3KBP1, HDAC2, RET, ABI1, LYN, GRB2, SORBS1, CLTC, CLTA, CDC42, CASP9, RAF1, SRC, AP2A1, AP2B1, MAPK3, ARHGEF7, PRKCA, RPS6, PRKAR2B, MAPK1, ARHGEF6, CDK1, SH3GL2, EIF4G1, HDAC1, ECT2, MKNK1, CASP3, PRKACA, ADRB2, PRKAR2A, EIF4B, SHC1, RAC1
2.77E-29 GO:0048011, Nerve growth factor receptor
signaling pathway
HDAC2, GRB2, CLTC, CLTA, CASP9, RAF1, SRC, AP2A1, AP2B1, MAPK3, ARHGEF7, PRKCA, PRKAR2B, MAPK1, ARHGEF6, CDK1,
SH3GL2, HDAC1, ECT2, CASP3, PRKACA, PRKAR2A, SHC1, RAC1 5.09E-24
GO:0007173, Epidermal growth factor receptor signaling pathway
SH3KBP1, GRB2, CLTC, CLTA, CDC42, CASP9, RAF1, SRC, AP2A1, AP2B1, MAPK3, ARHGEF7, PRKCA, PRKAR2B, MAPK1, CDK1,
SH3GL2, PRKACA, PRKAR2A, SHC1 2.96E-22
GO:0043067, Regulation of programmed cell death
HDAC2, STK17B, ESR1, ABL1, LYN, TP53, GABRB3, PAK2, LCK, CASP9, RAF1, PLK1, ARHGEF7, PRKCA, RPS6, SH3RF1, MAPK1, IFT57,
ARHGAP10, ARHGEF6, CDK1, APAF1, HDAC1, ECT2, CASP3, SOX10, EP300, ARAF, TFAP2A, ADRB2, HCK, KLHL20, CASP8, HIP1, RAC1 4.76E-19 GO:0042058, Regulation of epidermal
growth factor receptor signaling pathway SH3KBP1, ESR1, GRB2, CLTC, CLTA, CDC42, AP2A1, AP2B1, ARHGEF7, SH3GL2, SHC1 2.36E-12 GO:0008543, Fibroblast growth factor
receptor signaling pathway GRB2, CASP9, RAF1, SRC, MAPK3, PRKCA, PRKAR2B, MAPK1, CDK1, MKNK1, PRKACA, PRKAR2A, SHC1 2.39E-12 GO:0043068, Positive regulation of
programmed cell death
STK17B, ABL1, LYN, TP53, LCK, CASP9, ARHGEF7, PRKCA, RPS6, SH3RF1, MAPK1, ARHGEF6, APAF1, ECT2, CASP3, EP300, TFAP2A,
ADRB2, CASP8, HIP1, RAC1 3.09E-12
GO:0010942, Positive regulation of cell death
STK17B, ABL1, LYN, TP53, LCK, CASP9, ARHGEF7, PRKCA, RPS6, SH3RF1, MAPK1, ARHGEF6, APAF1, ECT2, CASP3, EP300, TFAP2A,
ADRB2, CASP8, HIP1, RAC1 4.49E-12
GO:0006917, Induction of apoptosis STK17B, ABL1, TP53, LCK, CASP9, ARHGEF7, PRKCA, SH3RF1, MAPK1, ARHGEF6, APAF1, ECT2, CASP3, EP300, CASP8, HIP1, RAC1 6.91E-11 GO:0012502, Induction of programmed
cell death STK17B, ABL1, TP53, LCK, CASP9, ARHGEF7, PRKCA, SH3RF1, MAPK1, ARHGEF6, APAF1, ECT2, CASP3, EP300, CASP8, HIP1, RAC1 7.42E-11
Table 6. Specific enriched GO terms of each miRNA-regulated PINs. (continue)
MIMAT0002856(hsa-miR-520d-3p)
GO term Genes Adj. p-value
GO:0042059, Negative regulation of epidermal growth factor receptor signaling pathway
SH3KBP1, GRB2, CLTC, CLTA, CDC42, AP2A1, AP2B1, ARHGEF7, SH3GL2 8.63E-11
GO:0015630, Microtubule cytoskeleton STMN1, SORBS1, SMAD4, CLTC, CDC42, LCK, RACGAP1, PLK1, PRKAR2B, YES1, MAPK1, IFT57, CDK1, ECT2, PRKACA, RB1, EP300,
CCNB1, CHAF1B, TFAP2A, CASP8, PRKAR2A 4.75E-10
GO:0060548, Negative regulation of cell
death HDAC2, ESR1, TP53, SMAD4, RAF1, PLK1, PRKCA, RPS6, SH3RF1, CDK1, HDAC1, CASP3, SOX10, ARAF, TFAP2A, HCK, KLHL20 6.27E-08 GO:0008286, Insulin receptor signaling
pathway GRB2, SORBS1, RAF1, MAPK3, RPS6, MAPK1, CDK1, EIF4G1, EIF4B, SHC1 2.15E-07
GO:0043069, Negative regulation of
programmed cell death HDAC2, ESR1, TP53, RAF1, PLK1, PRKCA, RPS6, SH3RF1, CDK1, HDAC1, CASP3, SOX10, ARAF, TFAP2A, HCK, KLHL20 3.13E-07 GO:0008284, Positive regulation of cell
proliferation HDAC2, ESR1, LYN, CDC42, E2F1, PRKCA, MAPK1, CDK1, RHOG, HDAC1, NCK1, SOX10, CCNB1, ADRB2, HCK, SHC1 8.34E-07 GO:0051988, Regulation of attachment of
spindle microtubules to kinetochore CDC42, RACGAP1, ECT2, CCNB1 3.27E-05
GO:0008629, Induction of apoptosis by
intracellular signals ABL1, TP53, CASP9, APAF1, CASP3, EP300, CASP8 5.83E-05
MIMAT0002820(hsa-miR-497-5p)
GO term Genes Adj. p-value
GO:0043067, Regulation of programmed cell death
ESR1, MEN1, ABL1, HIPK3, PPARGC1A, SIAH1, SH3RF1, PAK2, LCK, MED1, PPARG, CBX4, ARHGEF7, YWHAB, RXRA, ACVR1, MAPK1, CASP3, CASP6, AR, PTPRF, MDM2, BRCA1, MLH1, RAB27A, PIAS4, FAF1, RAC1, VHL, SKI, NR4A1, LYN, TP53, PSMC2, GATA1, GATA6, GATA3, RAF1, CDKN1B, PLK1, PSMD11, HOXA13, RPS6, ESR2, ARHGAP10, ARHGEF6, SMAD3, SKIL, RYR2, PSEN1, HCK, TRAF2
2.67E-25 GO:0043068, Positive regulation of
programmed cell death
MEN1, ABL1, SIAH1, SH3RF1, LCK, PPARG, ARHGEF7, YWHAB, RXRA, MAPK1, CASP3, CASP6, PTPRF, BRCA1, MLH1, RAB27A,
PIAS4, FAF1, RAC1, NR4A1, LYN, TP53, GATA6, CDKN1B, HOXA13, RPS6, ESR2, ARHGEF6, SMAD3, RYR2, PSEN1, TRAF2 1.74E-17 GO:0010942, Positive regulation of cell
death
MEN1, ABL1, SIAH1, SH3RF1, LCK, PPARG, ARHGEF7, YWHAB, RXRA, MAPK1, CASP3, CASP6, PTPRF, BRCA1, MLH1, RAB27A,
PIAS4, FAF1, RAC1, NR4A1, LYN, TP53, GATA6, CDKN1B, HOXA13, RPS6, ESR2, ARHGEF6, SMAD3, RYR2, PSEN1, TRAF2 3.08E-17
Table 6. Specific enriched GO terms of each miRNA-regulated PINs. (continue)
MIMAT0002820(hsa-miR-497-5p)
GO term Genes Adj. p-value
GO:0008285, Negative regulation of cell proliferation
MEN1, MED1, PPARG, RXRA, CASP3, AR, PTPRF, VDR, VHL, SKI, LYN, TP53, TOB1, GATA1, GATA3, RAF1, HNF4A, CDKN1B, BRD7,
MED25, ESR2, ABI1, SMAD1, SMAD2, SMAD3, SMAD4, SOX7 3.85E-14
GO:0015629, Actin cytoskeleton ABL1, SORBS1, FLNA, SEPT7, ANLN, MACF1, HAP1, SH3PXD2A, IQGAP2, BRCA1, ACTC1, ACTA1, MYL2, MYLK, SORBS2, ARPC4,
ARPC5, ACTR2, ACTR3, ARPC1B, WASF1, WASF2, HCK 2.52E-13
GO:0006917, Induction of apoptosis ABL1, SH3RF1, LCK, PPARG, ARHGEF7, YWHAB, MAPK1, CASP3, CASP6, BRCA1, MLH1, RAB27A, RAC1, NR4A1, TP53, CDKN1B,
ARHGEF6, SMAD3, RYR2, PSEN1, TRAF2 9.69E-11
GO:0012502, Induction of programmed cell death
ABL1, SH3RF1, LCK, PPARG, ARHGEF7, YWHAB, MAPK1, CASP3, CASP6, BRCA1, MLH1, RAB27A, RAC1, NR4A1, TP53, CDKN1B,
ARHGEF6, SMAD3, RYR2, PSEN1, TRAF2 1.06E-10
GO:0007178, Transmembrane receptor protein serine/threonine kinase signaling pathway
ACVR1, SMURF2, SKI, GDF6, BMP6, ZNF8, GATA4, HNF4A, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, RYR2 1.22E-10 GO:0007169, Transmembrane receptor
protein tyrosine kinase signaling pathway
SORBS1, CDC42, SRC, MAPK3, ARHGEF7, YWHAB, MAPK1, SH3GL2, CASP3, MDM2, EIF4G1, RAC1, SH3KBP1, NR4A1, LYN, GRB2,
RAF1, CDKN1B, RPS6, ABI1, ARHGEF6, MKNK1, PSEN1, EIF4B 1.67E-10
GO:0090092, Regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
MEN1, ACVR1, SMURF2, SKI, GDF6, TP53, BMP6, GATA4, GATA6, HOXA13, SMAD2, SMAD3, SMAD4, SKIL 7.51E-10
GO:0030509, BMP signaling pathway ACVR1, SMURF2, SKI, GDF6, BMP6, ZNF8, SMAD1, SMAD4, SMAD5, RYR2 3.25E-09
GO:0060548, Negative regulation of cell death
ESR1, HIPK3, PPARGC1A, SH3RF1, MED1, CBX4, ACVR1, CASP3, AR, MDM2, VHL, TP53, GATA1, GATA6, GATA3, RAF1, CDKN1B,
PLK1, RPS6, SMAD3, SMAD4, PSEN1, HCK 7.88E-09
GO:0007173, Epidermal growth factor
receptor signaling pathway CDC42, SRC, MAPK3, ARHGEF7, YWHAB, MAPK1, SH3GL2, MDM2, SH3KBP1, NR4A1, GRB2, RAF1, CDKN1B 9.22E-09 GO:0030521, Androgen receptor signaling
pathway PPARGC1A, MED14, MED1, AR, BRCA1, MED12, PIAS1, RAN, NR1I3 1.42E-08
GO:0043069, Negative regulation of programmed cell death
ESR1, HIPK3, PPARGC1A, SH3RF1, MED1, CBX4, ACVR1, CASP3, AR, MDM2, VHL, TP53, GATA1, GATA6, GATA3, RAF1, CDKN1B,
PLK1, RPS6, SMAD3, PSEN1, HCK 2.44E-08
GO:0048011, Nerve growth factor receptor
signaling pathway SRC, MAPK3, ARHGEF7, YWHAB, MAPK1, SH3GL2, CASP3, MDM2, RAC1, NR4A1, GRB2, RAF1, CDKN1B, ARHGEF6, PSEN1 2.64E-08 GO:0032956, Regulation of actin
cytoskeleton organization ABL1, LRP1, ARPC4, ARPC5, ACTR3, ARPC1B, SMAD3, NCK1, SORBS3, HCK, LIMK1 6.42E-06
Table 6. Specific enriched GO terms of each miRNA-regulated PINs. (continue)
MIMAT0002820(hsa-miR-497-5p)
GO term Genes Adj. p-value
GO:0008543, Fibroblast growth factor
receptor signaling pathway SRC, MAPK3, YWHAB, MAPK1, MDM2, NR4A1, GRB2, RAF1, CDKN1B, MKNK1 9.06E-06
GO:0042059, Negative regulation of epidermal growth factor receptor signaling pathway
CDC42, ARHGEF7, SH3GL2, PTPRF, SH3KBP1, GRB2, PSEN1 1.11E-05
GO:0042058, Regulation of epidermal
growth factor receptor signaling pathway ESR1, CDC42, ARHGEF7, SH3GL2, PTPRF, SH3KBP1, GRB2, PSEN1 1.17E-05
GO:0007179, Transforming growth factor
beta receptor signaling pathway ACVR1, SMURF2, SKI, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5 1.67E-05
GO:0015630, Microtubule cytoskeleton STMN1, RIF1, SORBS1, CDC42, LCK, RACGAP1, YES1, YWHAB, MAPK1, SEPT7, KIF23, CDC16, MACF1, BRCA1, FEZ1, NCOR1, PLK1,
CHD3, SMAD4, CEP350, CDC27, PSEN1 2.14E-05
GO:0017015, Regulation of transforming growth factor beta receptor signaling pathway
MEN1, SMURF2, SKI, TP53, SMAD2, SMAD3, SMAD4, SKIL 2.30E-05
GO:0070302, Regulation of
stress-activated protein kinase signaling cascade
MEN1, ZEB2, HIPK3, SH3RF1, CDC42, MAPK3, MAPK1, LYN, NCOR1, TRAF2 2.74E-05
GO:0001959, Regulation of
cytokine-mediated signaling pathway HSP90AB1, MED1, PPARG, PTPRF, NR1H2, PIAS1, IL36RN, HIPK1 6.35E-05
GO:0008284, Positive regulation of cell
proliferation ESR1, CDC42, MED1, RARA, MAPK1, AR, MDM2, NR4A1, LYN, FZR1, BMP6, GATA1, GATA4, GATA6, CDKN1B, NCK1, HCLS1, HCK 7.29E-05 MIMAT0000423(hsa-miR-125b-5p)
GO term Genes Adj. p-value
GO:0043067, Regulation of programmed cell death
HMGA2, PML, PRNP, FGF2, XRCC4, BRCA1, IGFBP3, HDAC3, CTNNB1, CD5, CDK1, NKX2-5, MEF2C, PRKCI, CASP2, PSMA4, PSMA3, CFDP1, CAV1, FAF1, YWHAB, HIF1A, RELA, TCF7L2, TNFSF12, PSEN2, TP53, TOP2A, TNFRSF4, BID, MYC, JUN, OGT, CDKN1A, HOXA13, RNF7, PPP2R4, HDAC2, HDAC1, SNCA, PTEN, NFKBIA, IFI16, NOL3, TRAF2, HSP90B1
4.56E-24 GO:0060548, Negative regulation of cell
death
HMGA2, PRNP, FGF2, XRCC4, HDAC3, CTNNB1, CDK1, NKX2-5, MEF2C, PRKCI, CFDP1, HIF1A, RELA, TCF7L2, PSEN2, TP53, TNFRSF4,
MYC, JUN, CDKN1A, RNF7, HDAC2, HDAC1, SNCA, PTEN, MGMT, NFKBIA, NOL3, HSP90B1 8.04E-17
GO:0008284, Positive regulation of cell proliferation
HMGA2, FGF2, XRCC4, CDC25B, CTNNB1, EGR1, AGGF1, CDK1, NKX2-5, MEF2C, PRKCI, IRS1, HIF1A, RELA, HCLS1, TNFSF12, ARNT,
PTPRC, TNFSF4, TNFRSF4, MYC, JUN, FGF1, CDKN1A, HDAC2, HDAC1, NOLC1, PTEN 2.20E-15
Table 6. Specific enriched GO terms of each miRNA-regulated PINs. (continue)
MIMAT0000423(hsa-miR-125b-5p)
GO term Genes Adj. p-value
GO:0043069, Negative regulation of programmed cell death
HMGA2, PRNP, XRCC4, HDAC3, CTNNB1, CDK1, NKX2-5, MEF2C, PRKCI, CFDP1, HIF1A, RELA, TCF7L2, PSEN2, TP53, TNFRSF4, MYC,
JUN, CDKN1A, RNF7, HDAC2, HDAC1, SNCA, PTEN, NFKBIA, NOL3, HSP90B1 3.62E-15
GO:0043068, Positive regulation of programmed cell death
HMGA2, PML, BRCA1, IGFBP3, CTNNB1, CD5, MEF2C, PRKCI, CASP2, CAV1, FAF1, YWHAB, TNFSF12, PSEN2, TP53, TOP2A, BID, JUN,
OGT, CDKN1A, HOXA13, RNF7, PPP2R4, PTEN, IFI16, TRAF2 4.51E-14
GO:0010942, Positive regulation of cell death
HMGA2, PML, BRCA1, IGFBP3, CTNNB1, CD5, MEF2C, PRKCI, CASP2, CAV1, FAF1, YWHAB, TNFSF12, PSEN2, TP53, TOP2A, BID, JUN,
OGT, CDKN1A, HOXA13, RNF7, PPP2R4, PTEN, IFI16, TRAF2 7.15E-14
GO:0006916, Anti-apoptosis PRNP, HDAC3, CDK1, NKX2-5, MEF2C, PRKCI, CFDP1, RELA, TCF7L2, PSEN2, RNF7, HDAC1, SNCA, NFKBIA, NOL3, HSP90B1 1.25E-10 GO:0008285, Negative regulation of cell
proliferation
SERPINF1, SRF, PML, PRNP, FGF2, CSNK2B, IGFBP3, CTNNB1, CAV1, HMGA1, VDR, CDH5, HSF1, COL18A1, TP53, MYC, JUN, CDKN1A,
PAK1, PTEN 2.08E-09
GO:0015630, Microtubule cytoskeleton STMN1, KIF1C, RANGAP1, CDC25B, BRCA1, HDAC3, CTNNB1, PIN4, HSPH1, RANBP9, CDK1, SPTAN1, YWHAQ, DVL1, FKBP4,
YWHAB, CCDC85B, MAPT, PSEN2, TOP2A, SPIB, MYC, OGT, APEX1, PAFAH1B1 2.24E-09
GO:0048011, Nerve growth factor receptor
signaling pathway HDAC3, CDK1, MEF2C, PRKCI, CASP2, IRS1, YWHAB, RELA, PSEN2, HDAC2, HDAC1, PTEN, ATF1, NFKBIA 1.99E-08 GO:0050678, Regulation of epithelial cell
proliferation SERPINF1, PGR, FGF2, CTNNB1, AGGF1, CAV1, HIF1A, TNFSF12, ARNT, MYC, JUN, FGF1, PTEN 3.41E-08
GO:0007169, Transmembrane receptor protein tyrosine kinase signaling pathway
FGF2, HDAC3, CDK1, MEF2C, PRKCI, CASP2, IRS1, FIBP, PTPN1, YWHAB, RELA, PSEN2, FGF1, HDAC2, HDAC1, PTEN, ATF1, NFKBIA,
EIF4EBP1 6.39E-08
GO:0006917, Induction of apoptosis PML, BRCA1, CD5, CASP2, CAV1, YWHAB, TNFSF12, PSEN2, TP53, BID, OGT, CDKN1A, RNF7, PTEN, IFI16, TRAF2 1.68E-07 GO:0012502, Induction of programmed
cell death PML, BRCA1, CD5, CASP2, CAV1, YWHAB, TNFSF12, PSEN2, TP53, BID, OGT, CDKN1A, RNF7, PTEN, IFI16, TRAF2 1.81E-07 GO:0035666, TRIF-dependent toll-like
receptor signaling pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 2.40E-06
GO:0034138, Toll-like receptor 3 signaling
pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 2.71E-06
GO:0051693, Actin filament capping SPTB, SPTBN1, SPTAN1, SPTA1, ADD1, EPB49 3.43E-06
Table 6. Specific enriched GO terms of each miRNA-regulated PINs. (continue)
MIMAT0000423(hsa-miR-125b-5p)
GO term Genes Adj. p-value
GO:0002756, MyD88-independent
toll-like receptor signaling pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 3.82E-06
GO:0034134, Toll-like receptor 2 signaling
pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 5.33E-06
GO:0034130, Toll-like receptor 1 signaling
pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 5.33E-06
GO:0030835, Negative regulation of actin
filament depolymerization SPTB, SPTBN1, SPTAN1, SPTA1, ADD1, EPB49 5.58E-06
GO:0015629, Actin cytoskeleton WAS, CDH1, BRCA1, SPTB, SPTBN1, SPTAN1, CTDP1, STX1A, SPTA1, PAK1, SNCA, ADD1, EPB41, EPB49 5.58E-06 GO:0002755, MyD88-dependent toll-like
receptor signaling pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 7.66E-06
GO:0034142, Toll-like receptor 4 signaling
pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 1.14E-05
GO:0050679, Positive regulation of
epithelial cell proliferation FGF2, CTNNB1, AGGF1, HIF1A, TNFSF12, ARNT, MYC, JUN, FGF1 1.14E-05
GO:0030834, Regulation of actin filament
depolymerization SPTB, SPTBN1, SPTAN1, SPTA1, ADD1, EPB49 1.27E-05
GO:0030837, Negative regulation of actin
filament polymerization SPTB, SPTBN1, SPTAN1, SPTA1, ADD1, EPB49 2.71E-05
GO:0002224, Toll-like receptor signaling
pathway ATF2, CDK1, MEF2C, FOS, RELA, JUN, ATF1, NFKBIA 2.96E-05
GO:0008629, Induction of apoptosis by
intracellular signals PML, BRCA1, YWHAB, TP53, BID, CDKN1A, RNF7, IFI16 3.52E-05
MIMAT0000076(hsa-miR-21-5p)
GO term Genes Adj. p-value
GO:0043067, Regulation of programmed
cell death SPRY2, TP53, ADAMTSL4, ETS1, TDGF1, RAF1, HOXA5, HOXA13, MSX1, MSX2, NKX2-5, CBL, INHBB, COL4A3, ACVR1C, TRAF2 1.92E-05
Table 6. Specific enriched GO terms of each miRNA-regulated PINs. (continue)
MIMAT0000076(hsa-miR-21-5p)
GO term Genes Adj. p-value
GO:0007173, Epidermal growth factor
receptor signaling pathway SPRY2, SPRY1, GRB2, PTPN11, TDGF1, RAF1, CBL 9.44E-05
MIMAT0000250(hsa-miR-139-5p)
GO term Genes Adj. p-value
GO:0035583, Negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta
LTBP1, FBN1, FBN2 2.61E-05
MIMAT0000089(hsa-miR-31-5p)
GO term Genes Adj. p-value
GO:0007187, G-protein signaling, coupled
to cyclic nucleotide second messenger GNA12, GNA13, DRD5, MTNR1A, S1PR3, TSHR, S1PR4 8.74E-07
GO:0019935, Cyclic-nucleotide-mediated
signaling GNA12, GNA13, DRD5, MTNR1A, S1PR3, TSHR, S1PR4 1.60E-06
GO:0007188, G-protein signaling, coupled
to cAMP nucleotide second messenger GNA12, GNA13, DRD5, S1PR3, TSHR, S1PR4 6.82E-06
GO:0048011, Nerve growth factor receptor
signaling pathway ARHGEF1, PRKCD, ARHGEF12, PRKACA, PRKCE, MCF2, ARHGEF11 6.93E-06
GO:0019933, CAMP-mediated signaling GNA12, GNA13, DRD5, S1PR3, TSHR, S1PR4 1.05E-05
GO:0043067, Regulation of programmed
cell death PTK2B, PRKCD, TGFBR1, ARHGEF12, CTNNB1, PRKCE, TIA1, MCF2, FASTK, ARHGEF11, F2R 1.25E-05
GO:0003376, Sphingosine-1-phosphate
signaling pathway S1PR3, S1PR2, S1PR4 3.22E-05
GO:0007169, Transmembrane receptor
protein tyrosine kinase signaling pathway PTK2B, ARHGEF1, PRKCD, ARHGEF12, PRKACA, PRKCE, MCF2, ARHGEF11 5.20E-05
protein tyrosine kinase signaling pathway PTK2B, ARHGEF1, PRKCD, ARHGEF12, PRKACA, PRKCE, MCF2, ARHGEF11 5.20E-05