From Oxidative Stress Damage to Pathways, Networks, and Autophagy via MicroRNAs

Table 2

Common pathways (KEGG) of microRNAs associated with oxidative stress. Common pathways (KEGG pathway IDs) of hsa-let7f (129 elements), hsa-miR-9 (140 elements), hsa-miR-16 (117 elements), hsa-miR-21 (64 elements), hsa-miR-22 (101 elements), hsa-miR-29b (126 elements), hsa-miR-99a (40 elements), hsa-miR-125b (126 elements), hsa-miR-128 (103 elements), hsa-miR-143 (80 elements), hsa-miR-144 (110 elements), hsa-miR-155 (70 elements), and hsa-miR-200c (113 elements). The pathways are common to all the 13 oxidative stress-modulated miRNAs. The KEGG pathway name (first column), the gene symbols involved in each pathway (second column), and the ID of the pathway used by the KEGG database (third column) are indicated. The database used for this analysis was DIANA-MicroT 3.0 [3].

KEGG pathway name	Gene symbol	KEGG pathway ID
MAPK signaling pathway	FGF12, PRKCA, MAP3K1, RPS6KA4, SOS1, MAP3K3, SRF, PAK2, MAP2K7, FGF18, RAP1B, MAPKAPK2, ACVR1B, TGFBR2, FGF5, DUSP6, ACVR1C, PDGFRB	hsa04010
Melanoma	FGF12, FGF18, FGF5, CDH1, IGF1, PDGFRB, PIK3R3, PDGFC	hsa05218
Colorectal cancer	RALGDS, SOS1, TCF7, ACVR1B, TGFBR2, ACVR1C, DCC, PDGFRB, PIK3R3, SMAD4	hsa05210
Glioma	PRKCA, SHC2, SOS1, SHC1, IGF1, PDGFRB, PIK3R3	hsa05214
Adherens junction	CTNNA1, ACTN2, VCL, TCF7, BAIAP2, SRC, ACVR1B, SSX2IP, TGFBR2, ACVR1C, CDH1, SMAD4	hsa04520
Focal adhesion	ITGB4, PRKCA, SHC2, ACTN2, TNC, DIAPH1, VCL, COL5A1, ITGA6, SOS1, VAV3, SHC1, SRC, PAK4, PAK2, PAK6, THBS2, RAP1B, IGF1, PDGFRB, PIK3R3, PDGFC	hsa04510
TGF-beta signaling pathway	ID4, SMURF1, INHBB, THBS2, ACVR1B, TGFBR2, ACVR1C, SMAD4	hsa04350
mTOR signaling pathway	TSC1, ULK2, IGF1, PIK3R3, EIF4E	hsa04150
Prostate cancer	CCNE2, SOS1, TCF7, FOXO1, CREB5, IGF1, PDGFRB, PIK3R3, PDGFC, CREB3L2	hsa05215
Wnt signaling pathway	WNT4, PRKCA, TCF7, VANGL1, PSEN1, PPARD, SMAD4	hsa04310
Cytokine-cytokine receptor interaction	LEP, CNTFR, LIFR, CXCL11, INHBB, KITLG, TNFRSF21, ACVR1B, TGFBR2, PDGFRB, PDGFC	hsa04060
Basal cell carcinoma	WNT4, TCF7, PTCH1	hsa05217
Type II diabetes mellitus	SOCS4, PIK3R3	hsa04930
Cell adhesion molecules (CAMs)	SDC2, CLDN14, SDC1, NFASC, ITGA6, NEO1, ALCAM, NLGN2, CDH1	hsa04514
Regulation of actin cytoskeleton	ITGB4, MYH9, FGF12, ACTN2, DIAPH1, VCL, ARPC1A, ARHGEF7, PIP4K2B, ITGA6, SOS1, VAV3, BAIAP2, DIAPH2, PAK4, PAK2, PAK6, FGF18, FGF5, SLC9A1, PDGFRB, PIK3R3	hsa04810
Long-term potentiation	PRKCA, RAP1B	hsa04720
Insulin signaling pathway	TSC1, SHC2, SOCS4, CBL, SOS1, FOXO1, SHC1, PIK3R3, EIF4E	hsa04910
Leukocyte transendothelial migration	CTNNA1, PRKCA, ACTN2, CLDN14, VCL, VAV3, RAP1B, PIK3R3	hsa04670
Tight junction	CTNNA1, MYH9, PPP2R4, PRKCA, ACTN2, CLDN14, AMOTL1, SRC, CSDA	hsa04530
Axon guidance	SRGAP3, PLXNA2, NTNG1, EPHB2, SEMA6D, EPHA7, NRP1, PAK4, PAK2, PAK6, DCC, EPHB4, EFNA1	hsa04360
Calcium signaling pathway	PRKCA, SLC8A1, ADCY9, PDGFRB	hsa04020
T cell receptor signaling pathway	CBL, SOS1, VAV3, PAK4, PAK2, PAK6, PIK3R3	hsa04660
GnRH signaling pathway	PRKCA, MAP3K1, SOS1, MAP3K3, SRC, ADCY9, MAP2K7	hsa04912
ErbB signaling pathway	PRKCA, SHC2, CBL, SOS1, SHC1, SRC, ABL2, PAK4, PAK2, PAK6, MAP2K7, PIK3R3	hsa04012
Acute myeloid leukemia	SOS1, TCF7, JUP, PPARD, PIK3R3	hsa05221
VEGF signaling pathway	PRKCA, SHC2, SRC, MAPKAPK2, PIK3R3	hsa04370

Note: see Supplementary Table 3 for this table in Excel format, and see Supplementary Table 4 for a full list of all KEGG pathways common to ≥2 of the 13 oxidative stress-modulated miRNAs.