Background
Methods
Patients and samples
Characteristics | N (%) |
---|---|
Age (year) (mean ± SD) | 68.66 ± 14.44 |
< 68 | 49 (41.53) |
≧68 | 69 (58.47) |
Sex | |
Male | 75 (63.56) |
Female | 43 (36.44) |
Race | |
White | 106 (89.83) |
Asian | 5 (4.24) |
Black or african american | 5 (4.24) |
Not available | 2 (1.69) |
Ethnicity | |
not hispanic or latino | 9 (7.63) |
hispanic or latino | 104 (88.13) |
not reported | 5 (4.24) |
Tumor stage | |
I | 13 (11.02) |
II | 20 (16.95) |
III | 27 (22.88) |
IVa | 56 (47.46) |
IVb | 2 (1.69) |
Survival status | |
Dead | 46 (38.98) |
Alive | 72 (61.02) |
RNA sequence analysis
Differentially expressed analysis
Functional enrichment analysis
Survival analysis
Construction of lncRNA-miRNA-mRNA ceRNA network
Results
Identification of differentially expressed lncRNA, miRNA and mRNA
Top 20 up-regulated mRNAs | |||
---|---|---|---|
mRNA | LogFC | P-Value | FDR |
TGFBI | 4.315537595 | 1.17E-25 | 4.22E-22 |
PLAU | 3.462663797 | 4.15E-25 | 9.92E-22 |
LAMC2 | 4.237080843 | 1.28E-23 | 1.54E-20 |
HOXC6 | 4.65525797 | 1.36E-21 | 1.15E-18 |
HOXA1 | 4.433954775 | 1.64E-21 | 1.31E-18 |
SERPINH1 | 2.639882646 | 3.24E-21 | 2.45E-18 |
COL4A2 | 2.81823357 | 3.44E-20 | 1.83E-17 |
HOXC11 | 5.695015733 | 4.79E-20 | 2.46E-17 |
COL4A1 | 3.133084242 | 1.36E-19 | 6.51E-17 |
COLGALT1 | 1.58936638 | 3.17E-19 | 1.42E-16 |
FSCN1 | 2.073990216 | 4.00E-19 | 1.74E-16 |
COL1A1 | 4.185143619 | 5.70E-19 | 2.27E-16 |
COL5A1 | 4.027658252 | 7.17E-19 | 2.78E-16 |
PTK7 | 2.001886655 | 8.17E-19 | 3.01E-16 |
COL12A1 | 3.740382035 | 2.85E-18 | 9.30E-16 |
MYO1B | 2.125906022 | 1.10E-17 | 3.36E-15 |
HOXC4 | 4.197008216 | 1.40E-17 | 4.18E-15 |
CD276 | 2.126335416 | 2.60E-17 | 7.18E-15 |
BMP1 | 2.44274785 | 2.87E-17 | 7.64E-15 |
PPP1R18 | 1.435370823 | 3.51E-17 | 8.55E-15 |
Top 20 up-regulated lncRNAs | |||
lncRNA | LogFC | P-Value | FDR |
AL358334.2 | 5.609527114 | 3.12E-24 | 6.30E-21 |
LINC02081 | 5.861313467 | 3.51E-24 | 6.30E-21 |
AC114956.2 | 4.026119266 | 1.38E-20 | 8.64E-18 |
LINC00941 | 4.887474201 | 8.07E-16 | 1.47E-13 |
AC002384.1 | 5.807235765 | 1.80E-15 | 2.90E-13 |
ZFPM2-AS1 | 5.506777453 | 5.05E-12 | 3.84E-10 |
LINC01615 | 4.417820628 | 9.78E-12 | 6.69E-10 |
GSEC | 2.402552017 | 3.38E-11 | 2.02E-09 |
LINC01322 | 5.896783476 | 1.57E-10 | 7.73E-09 |
AL024507.2 | 1.883167255 | 2.54E-10 | 1.17E-08 |
AL365356.5 | 3.477166051 | 6.36E-10 | 2.58E-08 |
FOXD2-AS1 | 2.111692628 | 7.75E-10 | 3.05E-08 |
MYOSLID | 3.218244344 | 1.68E-09 | 5.85E-08 |
TM4SF19-AS1 | 2.540840853 | 1.80E-08 | 4.44E-07 |
MIR503HG | 2.967470865 | 2.81E-08 | 6.42E-07 |
AC009948.1 | 1.233483122 | 2.81E-08 | 6.42E-07 |
AC099850.3 | 2.086563885 | 6.07E-08 | 1.25E-06 |
AC012073.1 | 1.49221094 | 6.69E-08 | 1.36E-06 |
U62317.2 | 3.239685972 | 7.99E-08 | 1.58E-06 |
LINC01116 | 2.92964907 | 1.23E-07 | 2.31E-06 |
Top 20 down-regulated mRNAs | |||
---|---|---|---|
mRNA | LogFC | P-Value | FDR |
CAB39L | −2.230860951 | 8.79E-30 | 1.26E-25 |
SH3BGRL2 | −4.129195634 | 4.15E-28 | 2.98E-24 |
FAM3D | −6.109712255 | 1.31E-27 | 6.29E-24 |
FUT6 | −5.441041935 | 2.63E-25 | 7.54E-22 |
GPD1L | −2.833273831 | 4.33E-24 | 6.91E-21 |
CYP4B1 | −5.201620597 | 5.94E-24 | 8.53E-21 |
SELENBP1 | −3.356944126 | 6.87E-24 | 8.97E-21 |
TLE2 | −3.218328165 | 1.65E-23 | 1.75E-20 |
CGNL1 | −3.633348282 | 1.70E-23 | 1.75E-20 |
HLF | −3.950815219 | 2.57E-22 | 2.47E-19 |
PAIP2B | −2.325857173 | 1.31E-21 | 1.15E-18 |
FMO2 | −4.962551951 | 4.23E-21 | 3.04E-18 |
TF | −5.192763131 | 9.20E-21 | 6.23E-18 |
RORC | −3.561163029 | 9.54E-21 | 6.23E-18 |
DEPTOR | −3.156822796 | 1.61E-20 | 9.61E-18 |
PLIN4 | −4.374193766 | 2.01E-20 | 1.16E-17 |
AGFG2 | −2.096127174 | 2.62E-20 | 1.45E-17 |
RRAGD | −3.179962858 | 6.47E-20 | 3.21E-17 |
FAM107A | −3.539763631 | 1.69E-19 | 7.81E-17 |
ALDH1A1 | −4.321886949 | 5.20E-19 | 2.20E-16 |
Top 20 down-regulated lncRNAs | |||
lncRNA | LogFC | P-Value | FDR |
ZNF710-AS1 | −2.097998239 | 1.42E-13 | 1.64E-11 |
AC104825.2 | −1.895549481 | 2.81E-12 | 2.27E-10 |
C5orf66 | −1.666569905 | 9.75E-11 | 5.11E-09 |
AL035661.1 | −2.362499591 | 1.75E-10 | 8.45E-09 |
WFDC21P | −2.838242509 | 4.55E-10 | 1.94E-08 |
AL691432.2 | −1.328157969 | 5.37E-09 | 1.57E-07 |
CBR3-AS1 | −1.384547792 | 1.41E-08 | 3.61E-07 |
DANCR | −1.479846155 | 1.49E-08 | 3.78E-07 |
LINC00957 | − 1.501952779 | 1.84E-08 | 4.50E-07 |
AC144831.1 | −1.8197168 | 1.92E-08 | 4.67E-07 |
EPB41L4A-AS1 | −1.119545231 | 1.97E-08 | 4.81E-07 |
AC009506.1 | −1.117948729 | 9.68E-08 | 1.86E-06 |
AC068888.1 | −1.291110108 | 3.26E-07 | 5.29E-06 |
ZNF667-AS1 | −1.77757381 | 4.94E-07 | 7.43E-06 |
AL357033.4 | −1.625781202 | 6.24E-07 | 9.13E-06 |
AC023283.1 | −1.450946619 | 8.16E-07 | 1.14E-05 |
AL109976.1 | −1.516544927 | 3.93E-06 | 4.27E-05 |
SPINT1-AS1 | −1.334348352 | 4.73E-06 | 4.98E-05 |
CEBPA-AS1 | −1.077762786 | 1.62E-05 | 0.000139196 |
LINC01133 | −2.012971887 | 2.62E-05 | 0.000209882 |
Top 20 up-regulated miRNAs | |||
---|---|---|---|
miRNA | LogFC | P-Value | FDR |
hsa-miR-21-5p | 1.679798023 | 7.95E-17 | 1.87E-14 |
hsa-miR-615-3p | 3.843177883 | 9.14E-15 | 8.61E-13 |
hsa-miR-455-3p | 2.783479203 | 4.93E-14 | 2.61E-12 |
hsa-miR-1301-3p | 1.837395098 | 1.08E-13 | 4.23E-12 |
hsa-miR-196b-5p | 3.706120237 | 5.20E-12 | 1.29E-10 |
hsa-miR-424-3p | 2.425887565 | 8.59E-12 | 2.02E-10 |
hsa-miR-877-5p | 2.426291524 | 4.51E-11 | 8.84E-10 |
hsa-miR-21-3p | 1.51590429 | 9.61E-11 | 1.68E-09 |
hsa-miR-503-5p | 3.129677768 | 1.40E-10 | 2.27E-09 |
hsa-miR-2355-5p | 1.702296959 | 1.70E-10 | 2.51E-09 |
hsa-miR-2355-3p | 1.998917306 | 6.52E-10 | 8.53E-09 |
hsa-miR-450a-5p | 1.904455832 | 1.38E-09 | 1.71E-08 |
hsa-miR-424-5p | 1.738999807 | 2.45E-09 | 2.88E-08 |
hsa-miR-224-5p | 2.165626373 | 4.47E-09 | 4.90E-08 |
hsa-miR-503-3p | 2.595299327 | 5.43E-09 | 5.82E-08 |
hsa-miR-671-5p | 1.663707163 | 5.65E-09 | 5.92E-08 |
hsa-miR-1307-3p | 1.345431238 | 3.09E-08 | 2.80E-07 |
hsa-miR-130b-5p | 1.368955234 | 3.42E-08 | 3.04E-07 |
hsa-miR-365a-5p | 2.405326455 | 7.33E-08 | 5.85E-07 |
hsa-miR-193b-3p | 1.581297442 | 1.22E-07 | 9.30E-07 |
Top 20 down-regulated miRNAs | |||
miRNA | LogFC | P-Value | FDR |
hsa-miR-101-3p | −2.332600896 | 1.63E-18 | 7.69E-16 |
hsa-miR-30a-5p | −2.147092552 | 1.97E-16 | 3.10E-14 |
hsa-miR-375 | −5.251608936 | 2.17E-15 | 2.55E-13 |
hsa-miR-30a-3p | −2.529446797 | 1.27E-14 | 9.94E-13 |
hsa-miR-99a-5p | −2.931395278 | 3.94E-14 | 2.61E-12 |
hsa-miR-204-5p | −3.385048334 | 4.99E-14 | 2.61E-12 |
hsa-miR-136-3p | −2.378717319 | 7.48E-14 | 3.52E-12 |
hsa-miR-378c | −2.529296096 | 9.57E-14 | 4.10E-12 |
hsa-miR-100-5p | −1.957154262 | 2.56E-13 | 9.26E-12 |
hsa-miR-30e-5p | −1.438413193 | 8.61E-13 | 2.90E-11 |
hsa-miR-29c-3p | −2.528703007 | 2.32E-12 | 7.28E-11 |
hsa-miR-99a-3p | −2.428873139 | 2.79E-12 | 8.20E-11 |
hsa-let-7c-5p | −2.56136633 | 3.70E-12 | 1.02E-10 |
hsa-miR-378a-5p | −1.993443856 | 9.76E-12 | 2.19E-10 |
hsa-miR-381-3p | −2.957588852 | 2.68E-11 | 5.75E-10 |
hsa-miR-101-5p | −1.711233075 | 4.18E-11 | 8.56E-10 |
hsa-miR-139-3p | −2.07771688 | 5.79E-11 | 1.09E-09 |
hsa-miR-299-5p | −2.309271223 | 9.31E-11 | 1.68E-09 |
hsa-miR-125b-5p | −1.382091675 | 1.30E-10 | 2.18E-09 |
hsa-miR-125b-2-3p | −2.491649904 | 1.50E-10 | 2.36E-09 |