Background
Methods
Retrieval of data and publications from TCGA and GEO
RT-qPCR
Statistical analysis
Differentially expressed mRNAs in LUSC based on TCGA
Selection of putative target genes of miR-198-5p
Bioinformatics analyses
Validation of the putative target genes in the most significant KEGG pathway based on TCGA data
Results
GEO data mining to determine the expression and diagnostic value of miR-198-5p
Var | Coeff. | Std. Err. | P value | RDOR | [95% CI] |
---|---|---|---|---|---|
Cte. | 0.123 | 0.782 | 0.8816 | – | – |
S | 0.5 | 0.2152 | 0.0679 | – | – |
Region | 1.221 | 0.4899 | 0.055 | 3.39 | (0.96;11.95) |
Clinical value of miR-198-5p in LUSC assessed using RT-qPCR
Clinicopathological feature |
n
| miR-198-5p expression (2−ΔCq) | |||
---|---|---|---|---|---|
Mean ± SD |
t
|
P
| |||
Tissue | LUSC | 23 | 4.3826 ± 1.7660 | 0.146 | 0.885 |
Non-tumor | 23 | 4.4522 ± 1.8263 | |||
Gender | Male | 18 | 4.4670 ± 1.8711 | 0.425 | 0.675 |
Female | 5 | 4.0800 ± 1.4584 | |||
Age | < 60 | 15 | 4.0930 ± 1.4270 | − 1.080 | 0.293 |
≥ 60 | 8 | 4.9250 ± 2.2833 | |||
Smoking state | No | 12 | 4.3000 ± 1.2884 | − 0.229 | 0.821 |
Yes | 11 | 4.4730 ± 2.2401 | |||
Size | ≤ 3 cm | 7 | 4.2570 ± 2.1196 | − 0.220 | 0.828 |
> 3 cm | 16 | 4.4380 ± 1.6633 | |||
EGFR amplification | No | 17 | 4.7470 ± 1.8084 | 1.741 | 0.096 |
Yes | 6 | 3.3500 ± 1.2357 | |||
Vascular invasion | No | 20 | 4.6100 ± 1.6914 | 1.656 | 0.113 |
Yes | 3 | 2.8670 ± 1.7786 | |||
TNM stage | I-II | 10 | 5.4400 ± 1.5277 | 2.917 | 0.008 |
III-IV | 13 | 3.5690 ± 1.5228 | |||
LNM | No | 11 | 4.8730 ± 2.0553 | 1.294 | 0.210 |
Yes | 12 | 3.9330 ± 1.3918 | |||
EGFR protein | Low | 18 | 4.3280 ± 1.9013 | − 0.277 | 0.785 |
High | 5 | 4.5800 ± 1.3142 | |||
MET | Low | 13 | 4.9230 ± 1.6559 | 1.750 | 0.095 |
High | 10 | 3.6800 ± 1.7313 | |||
Grading | II | 16 | 4.4130 ± 1.8326 | 0.12 | 0.906 |
III | 7 | 4.3140 ± 1.7411 |
Meta-analysis of miR-198-5p expression based on PCR and GEO data
Var | Coeff. | Std. Err. | P value | RDOR | [95%CI] |
---|---|---|---|---|---|
Cte. | 0.27 | 0.9327 | 0.7816 | – | – |
S | 0.125 | 0.1632 | 0.4714 | – | – |
Region | 0.751 | 0.5363 | 0.2107 | 2.12 | (0.57;7.88) |
Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, and protein-protein interaction (PPI) network
Category | Term | Count | P value |
---|---|---|---|
GOTERM_BP_DIRECT | GO:0008544~epidermis development | 10 | 4.84E−04 |
GOTERM_BP_DIRECT | GO:0043524~negative regulation of neuron apoptotic process | 12 | 9.35E−04 |
GOTERM_BP_DIRECT | GO:0008284~positive regulation of cell proliferation | 26 | 9.70E−04 |
GOTERM_BP_DIRECT | GO:0060070~canonical Wnt signaling pathway | 9 | 0.001824 |
GOTERM_BP_DIRECT | GO:0007399~nervous system development | 18 | 0.002211 |
GOTERM_BP_DIRECT | GO:0071277~cellular response to calcium ion | 7 | 0.002457 |
GOTERM_BP_DIRECT | GO:0007269~neurotransmitter secretion | 7 | 0.002457 |
GOTERM_BP_DIRECT | GO:0090103~cochlea morphogenesis | 5 | 0.002641 |
GOTERM_BP_DIRECT | GO:0014075~response to amine | 4 | 0.002773 |
GOTERM_BP_DIRECT | GO:0006366~transcription from RNA polymerase II promoter | 26 | 0.003531 |
GOTERM_CC_DIRECT | GO:0030054~cell junction | 29 | 7.60E−05 |
GOTERM_CC_DIRECT | GO:0005667~transcription factor complex | 15 | 9.32E−04 |
GOTERM_CC_DIRECT | GO:0008021~synaptic vesicle | 10 | 9.61E−04 |
GOTERM_CC_DIRECT | GO:0009986~cell surface | 29 | 0.001109 |
GOTERM_CC_DIRECT | GO:0045202~synapse | 13 | 0.004398 |
GOTERM_CC_DIRECT | GO:0005876~spindle microtubule | 6 | 0.006912 |
GOTERM_CC_DIRECT | GO:0042734~presynaptic membrane | 7 | 0.007013 |
GOTERM_CC_DIRECT | GO:0043195~terminal bouton | 7 | 0.007013 |
GOTERM_CC_DIRECT | GO:0098793~presynapse | 7 | 0.008171 |
GOTERM_CC_DIRECT | GO:0005887~integral component of plasma membrane | 55 | 0.008929 |
GOTERM_MF_DIRECT | GO:0046983~protein dimerization activity | 15 | 8.03E−05 |
GOTERM_MF_DIRECT | GO:0005509~calcium ion binding | 36 | 9.88E−04 |
GOTERM_MF_DIRECT | GO:0016810~hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds | 4 | 0.00922 |
GOTERM_MF_DIRECT | GO:0005109~frizzled binding | 5 | 0.017408 |
GOTERM_MF_DIRECT | GO:0001105~RNA polymerase II transcription coactivator activity | 5 | 0.019099 |
GOTERM_MF_DIRECT | GO:0043565~sequence-specific DNA binding | 24 | 0.019304 |
GOTERM_MF_DIRECT | GO:0008080~N-acetyltransferase activity | 4 | 0.022413 |
GOTERM_MF_DIRECT | GO:0003682~chromatin binding | 19 | 0.026956 |
GOTERM_MF_DIRECT | GO:0001077~transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding | 13 | 0.033582 |
GOTERM_MF_DIRECT | GO:0005262~calcium channel activity | 6 | 0.045673 |
Category | Term | Count | P value |
---|---|---|---|
KEGG_PATHWAY | hsa05223:Non-small cell lung cancer | 7 | 0.002996 |
KEGG_PATHWAY | hsa05200:Pathways in cancer | 20 | 0.005776 |
KEGG_PATHWAY | hsa05212:Pancreatic cancer | 7 | 0.006302 |
KEGG_PATHWAY | hsa05214:Glioma | 7 | 0.006302 |
KEGG_PATHWAY | hsa04512:ECM-receptor interaction | 8 | 0.00691 |
KEGG_PATHWAY | hsa04151:PI3K-Akt signaling pathway | 17 | 0.015931 |
KEGG_PATHWAY | hsa04360:Axon guidance | 9 | 0.016478 |
KEGG_PATHWAY | hsa05219:Bladder cancer | 5 | 0.020529 |
KEGG_PATHWAY | hsa05222:Small cell lung cancer | 7 | 0.021937 |
KEGG_PATHWAY | hsa04550:Signaling pathways regulating pluripotency of stem cells | 9 | 0.027765 |
KEGG_PATHWAY | hsa05166:HTLV-I infection | 13 | 0.032302 |
KEGG_PATHWAY | hsa05218:Melanoma | 6 | 0.035606 |
KEGG_PATHWAY | hsa00230:Purine metabolism | 10 | 0.037636 |
KEGG_PATHWAY | hsa04390:Hippo signaling pathway | 9 | 0.040805 |
KEGG_PATHWAY | hsa03410:Base excision repair | 4 | 0.05213 |
KEGG_PATHWAY | hsa00250:Alanine, aspartate and glutamate metabolism | 4 | 0.060271 |
KEGG_PATHWAY | hsa05206:MicroRNAs in cancer | 13 | 0.063619 |
KEGG_PATHWAY | hsa04014:Ras signaling pathway | 11 | 0.066327 |
KEGG_PATHWAY | hsa04724:Glutamatergic synapse | 7 | 0.073405 |
KEGG_PATHWAY | hsa05230:Central carbon metabolism in cancer | 5 | 0.082196 |
KEGG_PATHWAY | hsa05033:Nicotine addiction | 4 | 0.083009 |
KEGG_PATHWAY | hsa04510:Focal adhesion | 10 | 0.084102 |