Background
Materials
Data profile
Data pre-processing
Statistical analysis
Establishment of lncRNA–miRNA–mRNA ceRNA network
Functional annotation analysis
Nomogram construction
Results
Characteristics of included patients
Factor | Categories | Tumor status | Total | p-value | |
---|---|---|---|---|---|
Free | Recurred | ||||
Gender | Female | 10 | 53 | 63 | 0.361a |
Male | 5 | 45 | 50 | ||
Venous invasion | No | 11 | 73 | 84 | 0.924a |
Yes | 4 | 25 | 29 | ||
Lymphatic invasion | No | 9 | 48 | 57 | 0.427a |
Yes | 6 | 50 | 56 | ||
Pathology stage | I/II | 10 | 57 | 67 | 0.053a |
III/IV | 5 | 41 | 46 | ||
T stage | T1 | 0 | 3 | 3 | 0.151b |
T2 | 2 | 19 | 21 | ||
T3 | 9 | 64 | 73 | ||
T4 | 4 | 12 | 16 | ||
N0 | 10 | 58 | 68 | 0.295b | |
N stage | N1 | 4 | 19 | 23 | |
N2 | 1 | 21 | 22 | ||
M stage | M0 | 14 | 81 | 95 | 0.293a |
M1 | 1 | 17 | 18 | ||
Tumor site | Ascending colon | 4 | 20 | 24 | 0.009a |
Cecum | 7 | 18 | 25 | ||
Sigmoid colon | 1 | 42 | 43 | ||
Transverse colon | 3 | 7 | 10 | ||
Otherc | 0 | 11 | 11 | ||
Age at diagnosis | Mean | 65.33 | 71.95 | – | 0.049d |
SD | 12.26 | 11.93 | – |
Selection of different expressed RNA sequencing measurements
Establishment of lncRNA–miRNA–mRNA ceRNA network
lncRNA | Targeted miRNA |
---|---|
AC002310.1
| hsa-mir-129 |
AC139256.1
| hsa-mir-194 |
ACVR2B-AS1 | hsa-mir-125b, hsa-mir-141, hsa-mir-143, hsa-mir-182, hsa-mir-200a, hsa-mir-7 |
AL078459.1
| hsa-mir-145, hsa-mir-199a, hsa-mir-7 |
AL390066.1
| hsa-mir-106a, hsa-mir-141, hsa-mir-150, hsa-mir-200a, hsa-mir-205, hsa-mir-9, hsa-mir-93, hsa-mir-145, hsa-mir-29b, hsa-mir-29c |
AL391095.1
| hsa-mir-106a, hsa-mir-141, hsa-mir-150, hsa-mir-200a, hsa-mir-205, hsa-mir-9, hsa-mir-93, hsa-mir-145, hsa-mir-29b, hsa-mir-29c |
ALDH1L1-AS2 | hsa-mir-145 |
BCDIN3D-AS1 | hsa-mir-125b, hsa-mir-146b, hsa-mir-182, hsa-mir-18a, hsa-mir-205 |
CASC2
| hsa-mir-101, hsa-mir-106a, hsa-mir-125b, hsa-mir-141, hsa-mir-143, hsa-mir-15b, hsa-mir-16, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-193a, hsa-mir-193b, hsa-mir-194, hsa-mir-195, hsa-mir-200a, hsa-mir-200b, hsa-mir-200c, hsa-mir-204, hsa-mir-205, hsa-mir-21, hsa-mir-211, hsa-mir-33b, hsa-mir-34b, hsa-mir-34c, hsa-mir-424, hsa-mir-497, hsa-mir-506, hsa-mir-93 |
CCDC183-AS1 | hsa-let-7, hsa-mir-205, hsa-mir-205, hsa-mir-29b, hsa-mir-29c, hsa-mir-98 |
CTA-204B4.6 | hsa-let-7, hsa-mir-106a, hsa-mir-106b, hsa-mir-128, hsa-mir-129, hsa-mir-130a, hsa-mir-132, hsa-mir-135a, hsa-mir-135b, hsa-mir-142, hsa-mir-143, hsa-mir-145, hsa-mir-146b, hsa-mir-150, hsa-mir-15b, hsa-mir-16, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-195, hsa-mir-196a, hsa-mir-196b, hsa-mir-197, hsa-mir-200b, hsa-mir-200c, hsa-mir-204, hsa-mir-205, hsa-mir-211, hsa-mir-221, hsa-mir-29b, hsa-mir-29c, hsa-mir-301b, hsa-mir-30a, hsa-mir-30b, hsa-mir-30c, hsa-mir-30d, hsa-mir-33b, hsa-mir-34b, hsa-mir-34c, hsa-mir-424, hsa-mir-497, hsa-mir-92a, hsa-mir-92b, hsa-mir-93, hsa-mir-98 |
GRTP1-AS1 | hsa-mir-106a, hsa-mir-106b, hsa-mir-146b, hsa-mir-150, hsa-mir-93 |
HNRNPU-AS1 | hsa-mir-125b, hsa-mir-129, hsa-mir-132, hsa-mir-135a, hsa-mir-135b, hsa-mir-145, hsa-mir-145, hsa-mir-15b, hsa-mir-16, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-18a, hsa-mir-195, hsa-mir-199a, hsa-mir-204, hsa-mir-205, hsa-mir-211, hsa-mir-424, hsa-mir-497, hsa-mir-506 |
HOXA-AS3 | hsa-mir-106a, hsa-mir-106a, hsa-mir-106b, hsa-mir-125b, hsa-mir-132, hsa-mir-141, hsa-mir-143, hsa-mir-150, hsa-mir-15b, hsa-mir-16, hsa-mir-18a, hsa-mir-195, hsa-mir-200a, hsa-mir-204, hsa-mir-205, hsa-mir-211, hsa-mir-29b, hsa-mir-29c, hsa-mir-34b, hsa-mir-34c, hsa-mir-424, hsa-mir-497, hsa-mir-506, hsa-mir-7, hsa-mir-9, hsa-mir-93 |
HOTAIR
| hsa-mir-148b |
LINC00174
| hsa-mir-130a, hsa-mir-15b, hsa-mir-16, hsa-mir-195, hsa-mir-199a, hsa-mir-204, hsa-mir-211, hsa-mir-301b, hsa-mir-424, hsa-mir-497 |
LINC00641
| hsa-mir-129, hsa-mir-132, hsa-mir-135a, hsa-mir-135b, hsa-mir-145, hsa-mir-146b, hsa-mir-148a, hsa-mir-148b, hsa-mir-152, hsa-mir-15b, hsa-mir-16, hsa-mir-195, hsa-mir-200b, hsa-mir-200c, hsa-mir-204, hsa-mir-211, hsa-mir-221, hsa-mir-424, hsa-mir-497, hsa-mir-506, hsa-mir-7 |
LINC01089
| hsa-let-7, hsa-mir-128, hsa-mir-129, hsa-mir-135a, hsa-mir-135b, hsa-mir-145, hsa-mir-15b, hsa-mir-16, hsa-mir-193a, hsa-mir-193b, hsa-mir-195, hsa-mir-34b, hsa-mir-34c, hsa-mir-424, hsa-mir-497, hsa-mir-98 |
LINC02097
| hsa-mir-125b, hsa-mir-128, hsa-mir-143, hsa-mir-33b |
NORAD
| hsa-let-7, hsa-mir-101, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-182, hsa-mir-194, hsa-mir-199a, hsa-mir-204, hsa-mir-205, hsa-mir-211, hsa-mir-92a, hsa-mir-92b, hsa-mir-98 |
OIP5-AS1 | hsa-let-7, hsa-mir-130a, hsa-mir-132, hsa-mir-141, hsa-mir-143, hsa-mir-145, hsa-mir-146b, hsa-mir-148a, hsa-mir-148b, hsa-mir-150, hsa-mir-152, hsa-mir-15b, hsa-mir-16, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-18a, hsa-mir-194, hsa-mir-195, hsa-mir-196a, hsa-mir-196b, hsa-mir-200a, hsa-mir-200b, hsa-mir-200c, hsa-mir-205, hsa-mir-221, hsa-mir-223, hsa-mir-301b, hsa-mir-424, hsa-mir-497, hsa-mir-7, hsa-mir-98 |
PSMD6-AS2 | hsa-mir-106a, hsa-mir-135a, hsa-mir-135b, hsa-mir-141, hsa-mir-148a, hsa-mir-148b, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-182, hsa-mir-200a, hsa-mir-204, hsa-mir-211, hsa-mir-9, hsa-mir-93 |
RGMB-AS1 | hsa-mir-129, hsa-mir-143, hsa-mir-150, hsa-mir-34c, hsa-mir-7, hsa-mir-92a, hsa-mir-92b |
RP11-698N11.4 | hsa-mir-106a, hsa-mir-128, hsa-mir-132, hsa-mir-142, hsa-mir-148a, hsa-mir-148b, hsa-mir-152, hsa-mir-223, hsa-mir-34b, hsa-mir-34c, hsa-mir-7 |
SH3BP5-AS1 | hsa-mir-101, hsa-mir-106a, hsa-mir-125b, hsa-mir-132, hsa-mir-143, hsa-mir-146b, hsa-mir-15b, hsa-mir-16, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-182, hsa-mir-195, hsa-mir-199a, hsa-mir-200a, hsa-mir-204, hsa-mir-211, hsa-mir-223, hsa-mir-34b, hsa-mir-34c, hsa-mir-424, hsa-mir-497, hsa-mir-93 |
SLC25A25-AS1 | hsa-mir-150, hsa-mir-193a, hsa-mir-193b, hsa-mir-199a, hsa-mir-205, hsa-mir-34b, hsa-mir-34c, hsa-mir-9 |
STK4-AS1 | hsa-mir-106a, hsa-mir-106a, hsa-mir-106b, hsa-mir-182, hsa-mir-93 |
THUMPD3-AS1 | hsa-mir-143, hsa-mir-145, hsa-mir-146b, hsa-mir-15b, hsa-mir-16, hsa-mir-181a, hsa-mir-181c, hsa-mir-181d, hsa-mir-195, hsa-mir-221, hsa-mir-29b, hsa-mir-29c, hsa-mir-424, hsa-mir-497, hsa-mir-9 |
TTTY14
| hsa-mir-33b |
VPS9D1-AS1 | hsa-mir-135a, hsa-mir-135a, hsa-mir-135b |
miRNA | Targeted mRNA |
---|---|
hsa-let-7 |
AQP6, ASPSCR1, BEND4, BGLAP, CLEC4E, DCAF8, FGFRL1, FPR1, GGPS1, GPR141, HMGA2, IRF2BP2, JAG2, KCTD12, MDM4, NR2E1, NR6A1, NRM, PMF1, PPP1R16B, RS1, SF3B4, SPATA13, TOR1AIP2, TOR1AIP2, TRPV1, UBASH3B
|
hsa-mir-101 |
BEND4, CD180, CD180, GPR135, IL20RB, MNX1, TOR1AIP2
|
hsa-mir-106a |
CD28, CLEC12B, DCAF8, FOXQ1, FXYD5, HMGA2, KCND3, NUGGC, PRKCB, RAB42, RAB42, TLR7, TNIP3
|
hsa-mir-106b |
BAMBI, CCL1, CD28, CLEC12B, CYBB, DCAF8, EOMES, FOXQ1, FXYD5, GRAMD1A, KCND3, NUGGC, PRKCB, RAB42, TLR7, TNIP3
|
hsa-mir-125b |
BGLAP, PTAFR
|
hsa-mir-128 |
ASCL5, CYBB, IL21R
|
hsa-mir-129 |
HOXB8
|
hsa-mir-130a |
ATP6V1B2, FOXQ1, HOXB3, SNTB1
|
hsa-mir-132 |
CD226, CHL1, FUT1, KCNJ9, S100A1, SAMSN1, TNFRSF17
|
hsa-mir-135a |
LAX1, BGLAP
|
hsa-mir-141 | HLA-DRB1, HLA-DRB5, HOXB5, MALAT1, MDM4, STAT4 |
hsa-mir-142 |
CHRNA6, EVI2B, HMGA2, KCND3, KCTD12, LGR5, PIK3CG, PPP2R2C, PRKCB, SH2D1A, SIGLEC10, TNIP3, TOR1AIP2
|
hsa-mir-143 |
BAMBI, ENPP6, IL2RA, KLK2, LILRB1, MAPK8IP3, NKPD1, PHGDH, SLC16A10, TMEM40
|
hsa-mir-145 |
CD28, HMGA2, MMP1, MMP12, RTKN, SLC16A10, SNTB1
|
hsa-mir-146b |
MALAT1, PTGS1, TMPRSS5
|
hsa-mir-148a | HLA-DRB1, PAN3 |
hsa-mir-148b |
CCL19, CD300A, CPA3, CYBB, ENPP6, IL21R, KLRC1, PIK3CG, POU4F3, PSG9, SLC22A3
|
hsa-mir-150 |
CD96, CXCR4, FXYD5, MSRB2, NKD1, NUGGC, SRCIN1, TLR10, TLR7, TNIP3
|
hsa-mir-152 |
CD274
|
hsa-mir-15b |
ALDH3B1, BAMBI, CD180, CD274, FGFR4, HOXA3, IL20RB, IRF4, NAB1, NR6A1, POU2AF1, RS1, STX11
|
hsa-mir-16 |
CD226, HMGA2, INSL4
|
hsa-mir-181a |
CD4, CHL1, DCST1, GPR83, HMGA2, NR6A1, OFCC1, PRR4, RNF187, S100A1, SRGN, TAAR6, ZNF487
|
hsa-mir-181b |
HMGA2, NR6A1, RNF187, SH2D1A, SRGN, ZNF487
|
hsa-mir-181c |
HMGA2, KCNN3, NR6A1, RNF187, SRGN, ZNF487
|
hsa-mir-181d |
HMGA2, NR6A1, RNF187, SRGN, ZNF487
|
hsa-mir-182 |
CHL1, ZNF831
|
hsa-mir-18a |
DCAF8, MLXIPL, PTGS1, RHPN1, RNF187, RPL28, TEX22, ZNF33A
|
hsa-mir-193a |
FGF19, RTKN
|
hsa-mir-193b |
DOK2, FXYD5, PFDN2, PRPF40B, RTKN, ZNF366
|
hsa-mir-194 |
AQP6, CD274, HMGA2, MAPK8IP3, SLAMF1, SPATA13
|
hsa-mir-195 |
ALDH3B1, ALOX12, CD180, CD274, FGFR4, HOXA3, IRF4, NKD1, NR6A1, POU2AF1, RS1, UBE2E3
|
hsa-mir-196a |
ATP6V1B2, CXCL10, FUT1, HMGA2, HOXB8, NR6A1, TMEM78, TRPV1
|
hsa-mir-196b |
HMGA2, HOXB8, NR6A1, PIK3CG
|
hsa-mir-197 |
FPR1, NKD2, NKPD1
|
hsa-mir-199a |
CDKN1C, LAX1, POLR2F, SLC16A10, SNTB1, TOR1AIP2, UNC5C
|
hsa-mir-199b |
LAX1, POLR2F, SLC16A10, SNTB1, TOR1AIP2, UNC5C
|
hsa-mir-200a |
HOXB5, MALAT1, MDM4, MNX1, UBASH3B
|
hsa-mir-200b |
CD274, HOXB5, MALAT1, MDM4, TPD52L1
|
hsa-mir-200c |
CXCL10, HOXB5, MALAT1, POLR2F, TPD52L1
|
hsa-mir-204 | CCR5, CD28, CXCR4, CYBB, HLA-DRB1, HLA-DRB5, HMGA2, IRF2BP2, LY6G6F, MALAT1, TMEM156 |
hsa-mir-205 |
BAMBI, GPR141, IGSF6, ITM2A, PYHIN1
|
hsa-mir-21 |
CCL1, CXCL10, DCAF8, FGFRL1, FOXP3, GAS5, ITK, KLK2, MDM4, PAN3, RASGRP1, SLC16A10, TOR1AIP2, WFS1
|
hsa-mir-211 | ASCL2, CCR5, CD28, HLA-DRB1, HLA-DRB5, IL10RA, IRF2BP2, LY6G6F, RPL28, TMEM156, ZNF219 |
hsa-mir-221 |
CDKN1C, HOXB5, PTAFR
|
hsa-mir-223 |
CD226, GIMAP7, PAX6, PPP1R16B, TRAF5, UBE2E3
|
hsa-mir-29b |
IRF2BP2, KCTD12
|
hsa-mir-29c |
CD274, IRF2BP2, TARBP1, TESPA1
|
hsa-mir-301b | ATP6V1B2, CLEC12B, FOXQ1, HLA-DOA, HOXB3, LILRB2, SNTB1 |
hsa-mir-30a | ARG1, ATP6V1B2, BAMBI, FAM81B, HMGA2, IL21R, KCNN3, KRTAP5-9, MDM4, PTRH1, PYCR2 |
hsa-mir-30b |
AQP6, CD180, CD3D, CLEC7A, FAM81B, FGF19, GNG4, HAVCR2, IGSF6, IL21R, ITGA4, LAX1, MSRB2, MTA1, SCNM1, TOR1AIP2
|
hsa-mir-30c |
AQP6, CD180, CD3D, CLEC7A, FGF19, GNG4, HAVCR2, IGSF6, LAX1, MSRB2, SCNM1, TOR1AIP2
|
hsa-mir-30d |
AQP6, AQP6, CD3D, CLEC7A, FAM81B, GNG4, HAVCR2, IGSF6, IL21R, LAX1, MSRB2, RNF187, SCNM1, TOR1AIP2
|
hsa-mir-33b |
EVX2, HMGA2
|
hsa-mir-34b |
CD209, CD274, EBI3, MAK, POLR2F, TESPA1, ZNF831
|
hsa-mir-34c |
MDM4, PLA2G2D
|
hsa-mir-424 |
ALDH3B1, CD180, CD274, FGFR4, HOXA3, NR6A1, RGR, RS1
|
hsa-mir-497 |
ALDH3B1, CD180, CD274, EFNA3, EVX2, FGFR4, HOXA3, IRF4, NR6A1, RS1
|
hsa-mir-506 |
ENPP6, FOXQ1, HMGA2, TFEC
|
hsa-mir-7 |
MDM4, PFDN2, SPATA13
|
hsa-mir-9.3 |
CXCR4
|
hsa-mir-92a |
FGF19, KCNN3, MTA1, TESPA1
|
hsa-mir-92b |
CD180, CD226, CDKN1C, DAND5, FAM186A, HMGA2, LAX1, NUGGC, PYCR2, SRCIN1
|
hsa-mir-93 |
CCL1, CD28, CLEC12B, DCAF8, FOXQ1, FXYD5, GRAMD1A, KCND3, NUGGC, PFDN2, PRKCB, RAB42, TLR7, TNIP3, UNC5C
|
hsa-mir-98 |
BIRC3, CHRNA9, HMGA2, PIGC, TNFRSF9
|