Background
Methods
Patients’ samples
Sampling and RNA extraction
cDNA synthesis and quantitative RT-PCR
Gene name | Primer and probe sequence | Primer and probe length | Product length |
---|---|---|---|
HPRT1
| F: AGCCTAAGATGAGAGTTC | 18 | 88 |
R: CACAGAACTAGAACATTGATA | 21 | ||
FAM -CATCTGGAGTCCTATTGACATCGC- TAMRA | 24 | ||
NEAT1
| F: CCAGTGTGAGTCCTAGCATTGC | 20 | 78 |
R: CCTGGAAACAGAACATTGGAGAAC | 22 | ||
FAM- ACCCTGGAGGAGAGAGCCCGCC - TAMRA | 23 | ||
TUG1
| F: ACCGGAGGAGCCATCTTGTC | 24 | 149 |
R: GAAAGAGCCGCCAACCGATC | 24 | ||
FAM - ACCGCACGCCCGTTCCTTCGC -TAMRA | 24 | ||
FAS-AS1
| F: GAAAAGGTGCCGTTCTTCCG | 20 | 81 |
R: CTGGCAGTTCTCAGACGTAGG | 20 | ||
FAM - CGGCTTAACCACTGCTTCGGTGCT -TAMRA | 23 | ||
GAS5
| F: CTGCTTGAAAGGGTCTTGCC | 23 | 91 |
R: GGAGGCTGAGGATCACTTGAG | 23 | ||
FAM- ACCCAAGCTAGAGTGCAGTGGCCT- TAMRA | 24 | ||
PVT1
| F: CCCATTACGATTTCATCTC | 20 | 131 |
R: GTTCGTACTCATCTTATTCAA | 21 | ||
FAM- AGCAAGCACCTGTTACCTGTC - TAMRA | 20 | ||
HOTAIRM1
| F: GAAGAGCAAAAGCTGCGTTCTG | 22 | 135 |
R: CTCTCGCCAGTTCATCTTTCATTG | 24 | ||
FAM-CCCGACTCCGCTGCCCGCCC-TAMRA | 20 | ||
THRIL
| F: GAGTGCAGTGGCGTGATCTC | 20 | 121 |
R: AAAATTAGTCAGGCATGGTGGTG | 20 | ||
FAM- CTCACCGCAACCTCCACCTCCCAG- TAMRA | 23 |
Statistical analysis
In silico analyses
Results
General clinical and demographic data of patients
Gender N (%) | Smoking N (%) | Subtype N (%) | Stage N (%) | |||||
---|---|---|---|---|---|---|---|---|
Male | Female | Yes | No | Adenocarcinoma | Squamous cell carcinoma | 1 | 2 | 3 |
24 (75) | 8 (25) | 6 (18.75) | 26 (81.25) | 18 (56.25) | 14 (43.75) | 7 (21.88) | 11 (34.38) | 14 (43.75) |
Relative expression of lncRNAs in tumoral tissues vs. ANCTs
Total samples | Tissue samples from male patients | Tissue samples from female patients | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
REx | SE | Effect Size | P-value | 95% CrI | REx | SE | Effect Size | P-value* | 95% CrI* | REx | SE | Effect Size | P-value* | 95% CrI* | |
NEAT1
| 2.218 | 2.216 | 0.398 | 0.026 | [0.14, 4.32] | 3.027 | 1.33 | 0.502 | 0.038 | [0.15, 5.92] | 0.063 | 1.84 | 0.0145 | > 0.999 | [−3.93, 4.06] |
TUG1
| −2.798 | −2.8 | −0.744 | < 0.0001 | [−4.19, −1.38] | −2.76 | 0.881 | −0.694 | 0.004 | [−4.68, − 0.85] | − 2.971 | 1.6 | − 0.868 | 0.126 | [−6.45, 0.51] |
FAS-AS1
| −3.95 | 1.1 | −0.759 | 0.002 | [−6.14, − 1.76] | − 4.12 | 1.47 | − 0.68 | 0.03 | [−7.31, − 0.94] | − 3.147 | 1.58 | − 0.855 | 0.066 | [− 6.58, 0.29] |
GAS5
| −5.307 | 1.01 | − 0.997 | < 0.0001 | [−7.34, − 3.36] | −5.6 | 1.19 | −1.04 | < 0.0001 | [−8.19, − 3.02] | − 4.48 | 2.64 | −0.751 | 0.136 | [− 10.21, 1.25] |
PVT1
| − 2.123 | − 2.11 | − 0.404 | 0.034 | [−4.15, − 0.19] | − 2.104 | 1.15 | − 0.403 | 0.128 | [− 4.6, 0.4] | −2.171 | 2.72 | − 0.354 | 0.708 | [− 8.08, 3.74] |
THRIL
| −2.542 | 0.82 | − 0.583 | 0.002 | [−4.18, − 0.94] | − 2.93 | .995 | − 0.65 | 0.006 | [−5.09, − 0.78] | −1.405 | 1.93 | − 0.324 | 0.816 | [− 5.6, 2.79] |
HOTAIRM1
| − 2.347 | 0.71 | −0.622 | 0.001 | [− 3.74, − 0.93] | −2.381 | .86 | −0.608 | 0.012 | [−4.25, − 0.52] | − 2.285 | 1.72 | − 0.599 | 0.3 | [−6.02, 1.45] |
Association study of lncRNAs expression levels and clinicopathological data of patients
FAS-AS1 up-regulation | FAS-AS1 down-regulation | P value | HOTAIRM1 up-regulation | HOTAIRM1 Down-regulation | P value | NEAT1 up-regulation | NEAT1 down-regulation | P value | PVT1 up-regulation | PVT1 down-regulation | P value | THRIL up-regulation | THRIL down-regulation | P value | TUG1 up-regulation | TUG1 down-regulation | P value | GAS5 up-regulation | GAS5 down-regulation | P value | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Age | 1 | 0.48 | 0.48 | 0.723 | 0.476 | 0.723 | 0.723 | ||||||||||||||
< 60 years | 8(50%) | 8(50%) | 9 (56.3%) | 7(43.8%) | 9(56.2%) | 7(43.8) | 9(56.3%) | 7(43.8%) | 10(62.5%) | 6(37.5%) | 9(56.2%) | 7(43.8) | 7(43.8%) | 9(56.3%) | |||||||
≥60 years | 8(50%) | 8(50%) | 7(43.8%) | 9(56.3%) | 7(43.8) | 9(56.2%) | 8(50%) | 8(50%) | 8(50%) | 8(50%) | 8(50%) | 8(50%) | 8(50%) | 8(50%) | |||||||
Smoking | 1 | 1 | 1 | 1 | 0.426 | 0.272 | 0.678 | ||||||||||||||
Yes | 13(52%) | 12(48%) | 12(48%) | 13(52%) | 12(48%) | 13(52%) | 13(52%) | 12(48%) | 13(52%) | 12(48%) | 12(48%) | 13(52%) | 11(44%) | 14(56%) | |||||||
No | 3(42.9%) | 4(57.1%) | 4(57.1%) | 3(42.9%) | 4(57.1%) | 3(42.9%) | 4(57.1%) | 3(42.9%) | 5(71.4%) | 2(28.6%) | 5(71.4%) | 2(28.6%) | 4(57.1%) | 3(42.9%) | |||||||
Stage | 0.148 | 0.148 | 0.538 | 0.73 | 1 | 0.165 | 0.39 | ||||||||||||||
1 | 6(85.7%) | 1 (14.3%) | 6(85.7%) | 1 (14.3%) | 5(71.4%) | 2(28.6%) | 3(42.9%) | 4(57.1%) | 4(57.1%) | 3(42.9%) | 6(85.7%) | 1 (14.3%) | 5(71.4%) | 2(28.6%) | |||||||
2 | 4(36.4%) | 7(63.6%) | 4(36.4%) | 7(63.6%) | 5(45.5%) | 6(54.5%) | 7(63.6%) | 4(36.4%) | 6(54.5%) | 5(45.5%) | 5(45.5%) | 6(54.5%) | 4(36.4%) | 7(63.6%) | |||||||
3 | 6(42.9%) | 8(57.1%) | 6(42.9%) | 8(57.1%) | 6(42.9%) | 8(57.1%) | 7(50%) | 7(50%) | 8(57.1%) | 6(42.9%) | 6(42.9%) | 8(57.1%) | 6(42.9%) | 8(57.1%) | |||||||
Subtype | 0.476 | 1 | 1 | 0.688 | 0.53 | 0.688 | 0.305 | ||||||||||||||
Adenocarcinoma | 8(44.8%) | 10(55.6%) | 9 (50%) | 9 (50%) | 9 (50%) | 9 (50%) | 9 (50%) | 9 (50%) | 11(61.1%) | 7(38.9%) | 9 (50%) | 9 (50%) | 7(38.9%) | 11(61.1%) | |||||||
Squamous cell carcinoma | 8(57.1%) | 6 (42.9%) | 7 (50%) | 7 (50%) | 7 (50%) | 7 (50%) | 8 (57.1%) | 9 (42.9%) | 7 (50%) | 7 (50%) | 8 (57.1%) | 6 (42.9%) | 8(57.1%) | 6 (42.9%) |
lncRNAs | Parameters | Beta | SE | t | P-value | 95% CI for Beta |
---|---|---|---|---|---|---|
NEAT1
| Age | 0.04 | 0.13 | 0.28 | 0.78 | [−0.24, 0.31] |
Gender (Female/Male) | −1.62 | 2.33 | −0.70 | 0.49 | [−6.42, 3.17] | |
Smoking (Yes/No) | − 0.84 | 2.63 | −0.32 | 0.75 | [−6.26, 4.57] | |
Subtype (SCC/Adeno) | −2.64 | 1.99 | −1.32 | 0.20 | [−6.74, 1.46] | |
Stage | ||||||
2 | 0.71 | 2.62 | 0.27 | 0.79 | [−4.69, 6.1] | |
3 | 2.70 | 2.41 | 1.12 | 0.27 | [−2.26, 7.66] | |
TUG1
| Age | 0.19 | 0.11 | 1.64 | 0.11 | [−0.05, 0.42] |
Gender (Female/Male) | −3.78 | 2.00 | −1.89 | 0.07 | [−7.89, 0.33] | |
Smoking (Yes/No) | 1.74 | 2.26 | 0.77 | 0.45 | [−2.91, 6.39] | |
Subtype (SCC/Adeno) | −3.84 | 1.71 | −2.25 | 0.03 | [−7.36, −0.32] | |
Stage | ||||||
2 | 0.05 | 2.25 | 0.02 | 0.98 | [−4.57, 4.68] | |
3 | 0.84 | 2.06 | 0.41 | 0.69 | [− 3.41, 5.09] | |
FAS-AS1
| Age | 0.06 | 0.15 | 0.37 | 0.71 | [−0.26, 0.38] |
Gender (Female/Male) | 2.23 | 2.71 | 0.82 | 0.42 | [−3.34, 7.81] | |
Smoking (Yes/No) | −0.50 | 3.06 | −0.16 | 0.87 | [−6.81, 5.81] | |
Subtype (SCC/Adeno) | −0.71 | 2.32 | −0.31 | 0.76 | [−5.49, 4.06] | |
Stage | ||||||
2 | −0.61 | 3.05 | −0.20 | 0.84 | [−6.89, 5.67] | |
3 | 0.88 | 2.80 | 0.32 | 0.76 | [−4.88, 6.65] | |
GAS5
| Age | 0.14 | 0.13 | 1.06 | 0.30 | [−0.14, 0.42] |
Gender (Female/Male) | −0.84 | 2.36 | −0.36 | 0.72 | [−5.7, 4.02] | |
Smoking (Yes/No) | −2.55 | 2.67 | −0.96 | 0.35 | [−8.05, 2.95] | |
Subtype (SCC/Adeno) | −3.73 | 2.02 | −1.84 | 0.08 | [−7.89, 0.44] | |
Stage | ||||||
2 | 3.32 | 2.66 | 1.25 | 0.22 | [−2.16, 8.79] | |
3 | 3.52 | 2.44 | 1.44 | 0.16 | [−1.51, 8.55] | |
PVT1
| Age | 0.17 | 0.13 | 1.27 | 0.22 | [−0.1, 0.44] |
Gender (Female/Male) | −0.66 | 2.31 | −0.29 | 0.78 | [−5.42, 4.1] | |
Smoking (Yes/No) | −1.36 | 2.62 | −0.52 | 0.61 | [−6.74, 4.03] | |
Subtype (SCC/Adeno) | −1.74 | 1.98 | −0.88 | 0.39 | [−5.81, 2.34] | |
Stage | ||||||
2 | 0.69 | 2.60 | 0.27 | 0.79 | [−4.67, 6.05] | |
3 | 1.14 | 2.39 | 0.48 | 0.64 | [−3.78, 6.07] | |
THRIL
| Age | 0.01 | 0.16 | 0.07 | 0.95 | [−0.33, 0.35] |
Gender (Female/Male) | 0.52 | 2.87 | 0.18 | 0.86 | [−5.39, 6.44] | |
Smoking (Yes/No) | 0.00 | 3.25 | 0.00 | >.999 | [−6.69, 6.69] | |
Subtype (SCC/Adeno) | −2.77 | 2.46 | −1.13 | 0.27 | [−7.84, 2.29] | |
Stage | ||||||
2 | −3.20 | 3.23 | −0.99 | 0.33 | [−9.86, 3.46] | |
3 | 0.19 | 2.97 | 0.07 | 0.95 | [−5.93, 6.31] | |
HOTAIRM1
| Age | 0.46 | 0.24 | 1.94 | 0.06 | [−0.03, 0.96] |
Gender (Female/Male) | −1.92 | 4.19 | −0.46 | 0.65 | [−10.55, 6.72] | |
Smoking (Yes/No) | 3.57 | 4.74 | 0.75 | 0.46 | [−6.19, 13.33] | |
Subtype (SCC/Adeno) | − 6.50 | 3.59 | −1.81 | 0.08 | [−13.89, 0.89] | |
Stage | ||||||
2 | 0.64 | 4.72 | 0.14 | 0.89 | [−9.08, 10.36] | |
3 | 1.24 | 4.34 | 0.29 | 0.78 | [−7.68, 10.17] |
Correlation analysis between expression levels of lncRNAs in tumoral tissues and ANCTs
FAS-AS1
|
GAS5
|
PVT1
|
NEAT1
|
HOTAIRM1
|
TUG1
| ||
---|---|---|---|---|---|---|---|
THRIL
| Male | .639a | .770a | .524a | .585a | .455a | .549a |
Female | .603b | .653a | .244 | .403 | .594b | .412 | |
Tumor | .601a | .784a | .326 | .576a | .387b | .498a | |
ANCT | .318 | .447b | .32 | .495a | .353b | .335 | |
TUG1
| Male | .574a | .568a | .342b | .471a | .459a | |
Female | .638a | .812a | .612b | .394 | .506b | ||
Tumor | .606a | .75a | .464a | .687a | .464a | ||
ANCT | .282 | .170 | 0.53 | .181 | .345 | ||
HOTAIRM1
| Male | .491a | .408a | .395a | .470a | ||
Female | .509b | .565b | .185 | .209 | |||
Tumor | .432b | .533a | .266 | .446b | |||
ANCT | .221 | .052 | .388b | .333 | |||
NEAT1
| Male | .623a | .731a | .519a | |||
Female | .424 | .418 | .532b | ||||
Tumor | .749a | .785a | .746a | ||||
ANCT | .282 | .529a | .125 | ||||
PVT1
| Male | .468a | .345b | ||||
Female | .456 | .703a | |||||
Tumor | .622a | .699a | |||||
ANCT | .099 | .028 | |||||
GAS5
| Male | .770a | |||||
Female | .653a | ||||||
Tumor | .784a | ||||||
ANCT | .447b |
ROC curve analysis
Estimate criterion | AUC | Ja | Sensitivity | Specificity | P-valueb | |
---|---|---|---|---|---|---|
NEAT1
| > 0.13 | 0.676 | 0.312 | 75 | 56.25 | 0.008 |
TUG1
| ≤0.191 | 0.715 | 0.437 | 53.13 | 90.62 | 0.001 |
FAS-AS1
| ≤ − 2.82 | 0.764 | 0.5 | 59.38 | 90.62 | < 0.0001 |
GAS5
| ≤ − 1.991 | 0.884 | 0.625 | 81.25 | 81.25 | < 0.0001 |
PVT1
| ≤1.69 | 0.649 | 0.281 | 65.62 | 62.5 | 0.032 |
THRIL
| <−7.22 | 0.705 | 0.375 | 53.13 | 84.37 | 0.002 |
HOTAIRM1
| ≤ − 2.203 | 0.624 | 0.2813 | 31.25 | 96.87 | 0.081 |
KEGG pathway enrichment analysis
Term ID | Description | Genes | Count | % | P-value | False Discovery Rate |
---|---|---|---|---|---|---|
hsa05200 | Pathways in cancer | AKT1, BRAF, BCR, CREBBP, CRKL, KIT, TRAF3, ADCY4,ARNT, AXIN1, CTNNA1, COL4A3, CYCS, FZD6, GSK3B, LAMA4, LAMC1, PIK3R2, PTGER2, RBX1, STAT3, STAT5A, TCEB1 | 23 | 12.4 | 1.10E-05 | 2.50E-03 |
hsa05169 | Epstein-Barr virus infection | AKT1,CREBBP, POLR2H, POLR3C, POLR3K, TRAF3, XPO1, GSK3B, PIK3R2, PSMC6, PSMD11, PSMD14, STAT3, YWHAG | 14 | 7.6 | 1.10E-04 | 8.30E-03 |
hsa04110 | Cell cycle | BUB1, BUB3, CREBBP, ANAPC11, ANAPC2, CCNB1, GSK3B, ORC2, ORC3, RBX1, SMC3, YWHAG | 12 | 6.5 | 3.80E-05 | 4.10E-03 |
hsa05166 | HTLV-I infection | AKT1, BUB3, CREBBP, POLE, ADCY4, ANAPC11, ANAPC2, XPO1, FZD6, GSK3B, PIK3R2, STAT5A | 12 | 6.5 | 1.50E-02 | 1.50E-01 |
hsa03010 | Ribosome | RPL12, RPL30, RPL35, RPL37A, RPL38, RPL4, RPL8, RPS5, RPS7, RPS8, RPLP1 | 11 | 5.9 | 4.10E-04 | 1.80E-02 |
hsa05164 | Influenza A | AKT1, CREBBP, CYCS, XPO1, GSK3B, HNRNPUL1, PIK3R2, PABPN1, RAE1, SOCS3, TLR4 | 11 | 5.9 | 2.70E-03 | 7.10E-02 |
hsa03013 | RNA transport | RANBP2, RBM8A, UPF3A, EIF3J, EIF5B, XPO1, GEMIN4, GEMIN6, NUP205, RAE1 | 10 | 5.4 | 8.00E-03 | 1.10E-01 |
hsa05205 | Proteoglycans in cancer | AKT1, BRAF, IQGAP1, TIAM1, FZD6, PIK3R2, PPP1CC, PTPN6, STAT3, TLR4 | 10 | 5.4 | 2.00E-02 | 1.70E-01 |
hsa04932 | Non-alcoholic fatty liver disease | AKT1, NDUFB9, COX5A, COX7C, CYCS, GSK3B, PIK3R2, PRKAG1, SOCS3 | 9 | 4.9 | 1.10E-02 | 1.30E-01 |
hsa04062 | Chemokine signaling pathway | AKT1, BRAF, CRKL, TIAM1, ADCY4, GSK3B, PIK3R2, PRKCD, STAT3 | 9 | 4.9 | 3.50E-02 | 2.30E-01 |
hsa04510 | Focal adhesion | AKT1, BRAF, CRKL, COL4A3, GSK3B, LAMA4, LAMC1, PIK3R2, PPP1CC | 9 | 4.9 | 5.70E-02 | 3.10E-01 |
hsa04066 | HIF-1 signaling pathway | AKT1, CREBBP, ARNT, PIK3R2, RBX1, STAT3, TLR4, TCEB1 | 8 | 4.3 | 3.60E-03 | 8.30E-02 |
hsa04919 | Thyroid hormone signaling pathway | AKT1, CREBBP, GSK3B, MED13, NOTCH2, NOTCH4, NCOR1, PIK3R2 | 8 | 4.3 | 8.20E-03 | 1.00E-01 |
hsa05222 | Small cell lung cancer | AKT1, TRAF3, COL4A3, CYCS, LAMA4, LAMC1, PIK3R2 | 7 | 3.8 | 7.30E-03 | 1.10E-01 |
hsa04660 | T cell receptor signaling pathway | AKT1, CD4, GSK3B, LCP2, PIK3R2, PTPN6, PTPRC | 7 | 3.8 | 1.80E-02 | 1.60E-01 |
hsa04068 | FoxO signaling pathway | AKT1, BRAF, CREBBP, CCNB1, PIK3R2, PRKAG1, STAT3 | 7 | 3.8 | 5.40E-02 | 3.10E-01 |
hsa04630 | Jak-STAT signaling pathway | AKT1, CREBBP, PIK3R2, PTPN6, STAT3, STAT5A, SOCS3 | 7 | 3.8 | 7.40E-02 | 3.40E-01 |
hsa03015 | mRNA surveillance pathway | RBM8A, SMG1, SMG5, UPF3A, PABPN1, PPP1CC | 6 | 3.2 | 3.70E-02 | 2.40E-01 |
hsa04750 | Inflammatory mediator regulation of TRP channels | ADCY4, PIK3R2, PLA2G4F, PTGER2, PRKCD, PPP1CC | 6 | 3.2 | 4.80E-02 | 2.90E-01 |
hsa04330 | Notch signaling pathway | CREBBP, MAML2, NOTCH2, NOTCH4 | 4 | 2.2 | 7.30E-02 | 3.50E-01 |
GO analysis of differentially expressed target genes of lncRNAs in lung cancer
Category | Term | Count | % | P-value | False Discovery Rate |
---|---|---|---|---|---|
GOTERM_BP_DIRECT | GO:0007062~sister chromatid cohesion | 29 | 15.7 | 4.40E-05 | 5.60E-03 |
GOTERM_BP_DIRECT | GO:0000184~nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 15 | 8.1 | 4.80E-12 | 6.70E-09 |
GOTERM_BP_DIRECT | GO:0019083~viral transcription | 15 | 8.1 | 3.50E-11 | 2.50E-08 |
GOTERM_BP_DIRECT | GO:0006614~SRP-dependent cotranslational protein targeting to membrane | 15 | 8.1 | 3.10E-03 | 1.20E-01 |
GOTERM_BP_DIRECT | GO:0006413~translational initiation | 14 | 7.6 | 2.20E-10 | 1.00E-07 |
GOTERM_BP_DIRECT | GO:0051056~regulation of small GTPase mediated signal transduction | 14 | 7.6 | 2.10E-05 | 3.30E-03 |
GOTERM_BP_DIRECT | GO:0006364~rRNA processing | 14 | 7.6 | 1.10E-04 | 1.10E-02 |
GOTERM_BP_DIRECT | GO:0006412~translation | 13 | 7 | 2.80E-08 | 7.80E-06 |
GOTERM_BP_DIRECT | GO:0016032~viral process | 13 | 7 | 3.40E-06 | 6.90E-04 |
GOTERM_BP_DIRECT | GO:0006367~transcription initiation from RNA polymerase II promoter | 13 | 7 | 1.90E-05 | 3.30E-03 |
GOTERM_BP_DIRECT | GO:0007165~signal transduction | 12 | 6.5 | 5.00E-09 | 1.80E-06 |
GOTERM_BP_DIRECT | GO:0000132~establishment of mitotic spindle orientation | 11 | 5.9 | 1.80E-06 | 4.20E-04 |
GOTERM_BP_DIRECT | GO:0051301~cell division | 11 | 5.9 | 5.00E-02 | 5.90E-01 |
GOTERM_BP_DIRECT | GO:0051436~negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle | 11 | 5.9 | 5.10E-02 | 5.90E-01 |
GOTERM_BP_DIRECT | GO:0043488~regulation of mRNA stability | 11 | 5.9 | 8.50E-02 | 7.10E-01 |
GOTERM_BP_DIRECT | GO:0045860~positive regulation of protein kinase activity | 10 | 5.4 | 3.90E-05 | 5.40E-03 |
GOTERM_BP_DIRECT | GO:0051437~positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition | 10 | 5.4 | 1.50E-03 | 7.30E-02 |
GOTERM_BP_DIRECT | GO:0032869~cellular response to insulin stimulus | 10 | 5.4 | 3.00E-02 | 4.70E-01 |
GOTERM_BP_DIRECT | GO:0031145~anaphase-promoting complex-dependent catabolic process | 10 | 5.4 | 5.70E-02 | 6.00E-01 |
GOTERM_BP_DIRECT | GO:0016925~protein sumoylation | 9 | 4.9 | 1.60E-03 | 7.60E-02 |
GOTERM_BP_DIRECT | GO:0007052~mitotic spindle organization | 9 | 4.9 | 2.80E-03 | 1.10E-01 |
GOTERM_BP_DIRECT | GO:1990090~cellular response to nerve growth factor stimulus | 8 | 4.3 | 1.20E-04 | 1.10E-02 |
GOTERM_BP_DIRECT | GO:0071407~cellular response to organic cyclic compound | 8 | 4.3 | 2.70E-04 | 1.90E-02 |
GOTERM_BP_DIRECT | GO:0006406~mRNA export from nucleus | 8 | 4.3 | 2.30E-02 | 4.20E-01 |
GOTERM_BP_DIRECT | GO:0000082~G1/S transition of mitotic cell cycle | 8 | 4.3 | 9.90E-02 | 7.50E-01 |
GOTERM_BP_DIRECT | GO:1900034~regulation of cellular response to heat | 7 | 3.8 | 1.10E-04 | 1.10E-02 |
GOTERM_BP_DIRECT | GO:0007067~mitotic nuclear division | 7 | 3.8 | 1.60E-04 | 1.40E-02 |
GOTERM_BP_DIRECT | GO:0043161~proteasome-mediated ubiquitin-dependent protein catabolic process | 7 | 3.8 | 1.80E-04 | 1.40E-02 |
GOTERM_BP_DIRECT | GO:0006297~nucleotide-excision repair, DNA gap filling | 7 | 3.8 | 2.00E-04 | 1.50E-02 |
GOTERM_BP_DIRECT | GO:1901796~regulation of signal transduction by p53 class mediator | 7 | 3.8 | 7.20E-04 | 4.20E-02 |
GOTERM_BP_DIRECT | GO:0006368~transcription elongation from RNA polymerase II promoter | 7 | 3.8 | 8.00E-04 | 4.40E-02 |
GOTERM_BP_DIRECT | GO:0000070~mitotic sister chromatid segregation | 7 | 3.8 | 2.20E-03 | 9.80E-02 |
GOTERM_BP_DIRECT | GO:0000398~mRNA splicing, via spliceosome | 7 | 3.8 | 3.60E-03 | 1.30E-01 |
GOTERM_BP_DIRECT | GO:0043547~positive regulation of GTPase activity | 7 | 3.8 | 5.20E-03 | 1.70E-01 |
GOTERM_BP_DIRECT | GO:0061418~regulation of transcription from RNA polymerase II promoter in response to hypoxia | 7 | 3.8 | 6.50E-03 | 1.90E-01 |
GOTERM_BP_DIRECT | GO:0006661~phosphatidylinositol biosynthetic process | 7 | 3.8 | 8.30E-03 | 2.30E-01 |
r values | P values | |||
---|---|---|---|---|
adenocarcinoma | Squamous cell carcinoma | adenocarcinoma | Squamous cell carcinoma | |
GAS5 protein targets | ||||
IGF2BP2 | −0.32657 | NS | 4.38064e-15 | NS |
TNRC6 | −0.24924 | −0.09044 | 3.3202e-09 | 0.036 |
eIF4AIII | 0.23814 | 0.24445 | 1.66706e-08 | 1.08209e-08 |
FXR1 | NS | 0.21644 | NS | 4.53143e-07 |
ZC3H7B | −0.39888 | − 0.3438 | 2.41224e-22 | 3.11115e-16 |
TIA1 | 0.30713 | 0.36671 | 1.95659e-13 | 2.0744e-18 |
TIAL1 | 0.40815 | 0.5783 | 2.05785e-23 | 0 |
hnRNPC | 0.53945 | 0.49973 | 1.05658e-42 | 5.11375e-35 |
UPF1 | −0.18416 | −0.15503 | 1.43503e-05 | 0.0003 |
PVT1 protein targets | ||||
PTB | 0.21781 | 0.3321 | 2.61794e-07 | 3.44464e-15 |
eIF4AIII | 0.34272 | 0.41381 | 1.5088e-16 | 1.82621e-23 |
FUS | 0.14317 | 0.23924 | 0.0007 | 2.24886e-08 |
SFRS1 | 0.32099 | 0.34682 | 1.34165e-14 | 1.64563e-16 |
U2AF65 | 0.28095 | 0.34364 | 2.12424e-11 | 3.21989e-16 |
TIA1 | 0.29682 | 0.17857 | 1.31293e-12 | 3.38048e-05 |
TIAL1 | 0.36842 | 0.43761 | 4.64078e-19 | 2.42026e-26 |
hnRNPC | 0.41684 | 0.4676 | 1.90385e-24 | 2.61554e-30 |
NEAT1 protein targets | ||||
IGF2BP3 | −0.23744 | NS | 1.84153e-08 | NS |
TNRC6 | 0.63612 | 0.57187 | 0 | 0 |
eIF4AIII | −0.24738 | − 0.21657 | 4.37988e-09 | 4.45995e-07 |
DGCR8 | 0.47992 | 0.40956 | 6.47436e-33 | 5.65318e-23 |
FUS | 0.15949 | 0.28231 | 0.0001 | 3.18582e-11 |
C22ORF28 | −0.41602 | −0.39928 | 2.39532e-24 | 8.11096e-22 |
EWSR1 | 0.45642 | 0.38323 | 1.49592e-29 | 4.32566e-20 |
FUS-mutant | 0.15949 | 0.28231 | 0.0001 | 3.18582e-11 |
TAF15 | 0.35774 | 0.30791 | 5.4777e-18 | 3.61613e-13 |
TIA1 | 0.39134 | 0.14772 | 1.68868e-21 | 0.0006 |
hnRNPC | −0.30402 | −0.30302 | 3.50144e-13 | 8.79981e-13 |
UPF1 | 0.26028 | 0.23562 | 6.17422e-10 | 3.69822e-08 |
TDP43 | 0.35409 | 0.27796 | 1.24663e-17 | 6.51646e-11 |
TUG1 protein targets | ||||
HuR | 0.23073 | 0.24185 | 4.68727e-08 | 1.56196e-08 |
PTB | 0.23828 | 0.36496 | 1.6354e-08 | 3.08972e-18 |
IGF2BP1 | 0.20216 | 0.20823 | 1.83405e-06 | 1.23854e-06 |
IGF2BP2 | 0.11891 | 0.29403 | 0.005 | 4.32685e-12 |
IGF2BP3 | 0.106 | 0.24703 | 0.01304 | 7.48794e-09 |
PUM2 | 0.37119 | 0.40428 | 2.41171e-19 | 2.2431e-22 |
TNRC6 | 0.61159 | 0.49489 | 0 | 2.81834e-34 |
DGCR8 | 0.65857 | 0.56409 | 0 | 0 |
FMRP | 0.26472 | 0.1925 | 3.06394e-10 | 7.61715e-06 |
FXR1 | 0.20584 | 0.37095 | 1.17509e-06 | 7.86123e-19 |
FUS | 0.28187 | 0.29685 | 1.8177e-11 | 2.64246e-12 |
MOV10 | 0.28645 | 0.17153 | 8.25055e-12 | 6.88368e-05 |
ZC3H7B | 0.44562 | 0.40705 | 4.31803e-28 | 1.09058e-22 |
EWSR1 | 0.59372 | 0.52829 | 0 | 1.20774e-39 |
FUS-mutant | 0.28187 | 0.29685 | 1.8177e-11 | 2.64246e-12 |
SFRS1 | 0.42337 | 0.3621 | 3.04287e-25 | 5.87589e-18 |
U2AF65 | 0.10951 | 0.21837 | 0.01 | 3.55695e-07 |
hnRNPC | −0.21224 | −0.1016 | 5.32579e-07 | 0.0188867 |
UPF1 | 0.3765 | 0.41283 | 6.73768e-20 | 2.37266e-23 |
TDP43 | 0.5917 | 0.4423 | 0 | 6.1369e-27 |