Table 2.
Differentially expressed levels and genomic alterations of mRNAs in the ceRNA regulatory network in SCLC.
| Gene symbol | Gene full name | Differentially expressed levels | Genomic alterations | ||||||
|---|---|---|---|---|---|---|---|---|---|
| In-house SCLC plasma cohort | SCLC lung tissue cohort (GSE40275) | Regulated | CLCGP, Nat Genet 2012 | Johns Hopkins, Nat Genet 2012 | U Cologne,Nature 2015 | ||||
| log2FC | p value | log2FC | p value | ||||||
| Genomic alterations (n = 50) | |||||||||
| EGR1 | Early Growth Response 1 | -3.232 | 2.30E-04 | -2.611 | 3.42E-16 | down | 3.0% | 0 | 0 |
| CFD | Complement Factor D | -2.898 | 2.11E-02 | -2.472 | 2.01E-25 | down | 0 | 0 | 0.8% |
| ABCA2 | ATP Binding Cassette Subfamily A Member 2 | -2.814 | 3.54E-03 | -1.923 | 3.00E-04 | down | 3.0% | 1.3% | 2.5% |
| PRF1 | Perforin 1 | -2.699 | 5.32E-04 | -2.038 | 5.60E-20 | down | 3.0% | 0 | 1.7% |
| STAB1 | Stabilin 1 | -2.484 | 2.34E-04 | -1.151 | 2.39E-14 | down | 3.0% | 0 | 4.0% |
| AHNAK | AHNAK Nucleoprotein | -2.443 | 6.74E-06 | -2.761 | 8.93E-29 | down | 7.0% | 4.0% | 6.0% |
| CD300E | CD300e Molecule | -2.428 | 7.77E-05 | -1.009 | 3.72E-15 | down | 0 | 0 | 0.8% |
| CD244 | CD244 Molecule | -2.332 | 2.57E-02 | -0.751 | 3.88E-15 | down | 3.0% | 0 | 0.8% |
| SLC27A1 | Solute Carrier Family 27 Member 1 | -2.331 | 3.90E-02 | -0.76 | 6.68E-14 | down | 7.0% | 1.3% | 1.7% |
| PARP10 | Poly (ADP-Ribose) Polymerase Family Member 10 | -2.12 | 2.62E-02 | -0.601 | 4.27E-10 | down | 3.0% | 0 | 0.8% |
| MEFV | MEFV Innate Immuity Regulator, Pyrin | -2.051 | 9.52E-03 | -1.031 | 2.62E-19 | down | 0 | 1.3% | 1.7% |
| RHBDF2 | Rhomboid 5 Homolog 2 | -2.028 | 3.29E-02 | -0.981 | 5.62E-14 | down | 3.0% | 0 | 0 |
| DNAH1 | Dynein Axonemal Heavy Chain 1 | -2.02 | 1.14E-02 | -0.653 | 2.03E-18 | down | 0 | 0 | 7.0% |
| TCIRG1 | T Cell Immune Regulator 1, ATPase H+ Transporting V0 Subunit A3 | -1.998 | 9.10E-03 | -1.421 | 4.46E-17 | down | 0 | 0 | 1.7% |
| NFAM1 | NFAT Activating Protein With ITAM Motif 1 | -1.976 | 4.41E-02 | -0.708 | 2.61E-13 | down | 0 | 1.3% | 0.8% |
| GIMAP8 | GTPase, IMAP Family Member 8 | -1.902 | 1.10E-02 | -2.078 | 2.10E-31 | down | 10.0% | 0 | 3.0% |
| PLXNB2 | Plexin B2 | -1.896 | 3.39E-03 | -1.094 | 1.38E-09 | down | 7.0% | 1.3% | 3.0% |
| FGD2 | FYVE, RhoGEF And PH Domain Containing 2 | -1.885 | 3.07E-03 | -1.384 | 7.07E-19 | down | 0 | 0 | 0.8% |
| NLRP12 | NLR Family Pyrin Domain Containing 12 | -1.862 | 2.96E-02 | -0.852 | 4.45E-16 | down | 7.0% | 1.3% | 4.0% |
| NOTCH1 | Notch Receptor 1 | -1.848 | 2.58E-02 | -1.497 | 3.76E-22 | down | 10.0% | 1.3% | 13.0% |
| FCN1 | Ficolin 1 | -1.844 | 7.66E-03 | -1.675 | 3.00E-23 | down | 0 | 0 | 2.5% |
| CSF3R | Colony-stimulating factor 3 receptor | -1.801 | 2.63E-03 | -2.469 | 2.01E-29 | down | 7.0% | 1.3% | 2.5% |
| GAA | Acid alpha-glucosidase | -1.789 | 3.85E-02 | -1.108 | 5.29E-13 | down | 3.0% | 1.3% | 2.5% |
| ITGB2 | Integrin Subunit Beta 2 | -1.756 | 9.89E-03 | -1.813 | 1.26E-11 | down | 3.0% | 0 | 2.5% |
| EMILIN2 | Elastin Microfibril Interfacer 2 | -1.748 | 8.86E-03 | -1.372 | 1.79E-18 | down | 0 | 2.5% | 2.5% |
| ARHGAP4 | Rho GTPase Activating Protein 4 | -1.741 | 1.37E-02 | -0.624 | 3.80E-07 | down | 3.0% | 1.3% | 4.0% |
| CD93 | CD93 Molecule | -1.722 | 2.15E-02 | -2.668 | 4.54E-34 | down | 3.0% | 0 | 1.7% |
| DAPK1 | Death Associated Protein Kinase 1 | -1.707 | 1.97E-02 | -1.123 | 5.50E-05 | down | 3.0% | 2.5% | 4.0% |
| TTC7A | Tetratricopeptide Repeat Domain 7A | -1.651 | 2.83E-02 | -1.265 | 3.85E-20 | down | 0 | 1.3% | 2.5% |
| PSD4 | Pleckstrin And Sec7 Domain Containing 4 | -1.632 | 1.74E-02 | -0.802 | 3.80E-11 | down | 3.0% | 1.3% | 3.0% |
| CIITA | Class II Major Histocompatibility Complex Transactivator | -1.624 | 2.17E-03 | -1.777 | 3.50E-17 | down | 0 | 1.3% | 0 |
| SYNE1 | Spectrin Repeat Containing Nuclear Envelope Protein 1 | -1.606 | 3.16E-03 | -1.689 | 1.78E-19 | down | 28.0% | 11.0% | 23.0% |
| ITGAX | Integrin Subunit Alpha X | -1.592 | 1.15E-02 | -2.083 | 9.75E-18 | down | 3.0% | 1.3% | 3.0% |
| ADAMTSL4 | ADAMTS Like 4 | -1.555 | 3.60E-02 | -1.606 | 2.64E-22 | down | 0 | 0 | 2.5% |
| XAF1 | XIAP Associated Factor 1 | -1.552 | 1.88E-02 | -1.445 | 3.44E-10 | down | 3.0% | 1.3% | 0 |
| FGR | FGR Proto-Oncogene, Src Family Tyrosine Kinase | -1.488 | 2.02E-02 | -2.179 | 5.88E-22 | down | 0 | 2.5% | 0.8% |
| PLCB2 | Phospholipase C Beta 2 | -1.474 | 1.89E-02 | -1.634 | 8.74E-19 | down | 0 | 1.3% | 0 |
| APLP2 | Amyloid Beta Precursor Like Protein 2 | -1.47 | 2.22E-02 | -0.935 | 5.30E-17 | down | 5.0% | 2.5% | 0 |
| AKNA | AT-Hook Transcription Factor | -1.467 | 4.69E-02 | -1.126 | 7.79E-20 | down | 7.0% | 2.5% | 1.7% |
| RNF213 | Ring Finger Protein 213 | -1.452 | 1.46E-02 | -0.714 | 8.47E-06 | down | 0 | 4.0% | 2.5% |
| HERC3 | HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 3 | -1.45 | 4.01E-02 | -0.725 | 1.92E-16 | down | 0 | 0 | 0.8% |
| ARHGEF1 | Rho Guanine Nucleotide Exchange Factor 1 | -1.443 | 3.72E-02 | -0.724 | 6.28E-09 | down | 0 | 1.3% | 2.5% |
| MYO1F | Myosin 1F | -1.394 | 4.04E-02 | -2.014 | 2.90E-22 | down | 3.0% | 1.3% | 2.5% |
| MYO1G | Myosin 1G | -1.314 | 3.45E-02 | -1.526 | 3.29E-20 | down | 3.0% | 0 | 1.7% |
| ADCY7 | Adenylate Cyclase 7 | -1.314 | 3.64E-02 | -1.626 | 7.20E-23 | down | 3.0% | 0 | 4.0% |
| PARP14 | Poly(ADP-Ribose) Polymerase Family Member 14 | -1.233 | 4.09E-02 | -1.178 | 2.66E-08 | down | 0 | 0 | 2.5% |
| ITGAL | Integrin Subunit Alpha L | -1.225 | 3.83E-02 | -1.893 | 6.38E-17 | down | 3.0% | 0 | 5.0% |
| ZNF704 | Zinc Finger Protein 704 | Inf | 2.00E-02 | 1.059 | 8.34E-13 | up | 0 | 0 | 0.8% |
| NOVA1 | NOVA Alternative Splicing Regulator 1 | Inf | 3.63E-02 | 1.039 | 2.61E-16 | up | 0 | 1.3% | 1.7% |
| ATRNL1 | Attractin Like 1 | Inf | 3.34E-02 | 0.878 | 6.12E-09 | up | 7.0% | 4.0% | 3.0% |
| No genomic alterations (n = 8) | |||||||||
| FOSB | FosB Proto-Oncogene, AP-1 Transcription Factor Subunit | -3.723 | 4.45E-02 | -3.385 | 2.01E-15 | down | 0 | 0 | 0 |
| ADAM15 | ADAM Metallopeptidase Domain 15 | -3.479 | 1.29E-02 | -0.586 | 4.13E-08 | down | 0 | 0 | 0 |
| KLF6 | Kruppel Like Factor 6 | -1.999 | 4.21E-03 | -1.665 | 3.59E-18 | down | 0 | 0 | 0 |
| IL10RA | Interleukin 10 Receptor Subunit Alpha | -1.921 | 2.54E-03 | -1.772 | 8.82E-14 | down | 0 | 0 | 0 |
| ATG16L2 | Autophagy Related 16 Like 2 | -1.851 | 0.01755 | -0.665 | 1.89E-12 | down | 0 | 0 | 0 |
| MYO15B | Myosin XVB | -1.814 | 4.40E-02 | -0.837 | 1.26E-12 | down | 0 | 0 | 0 |
| IRF1 | Interferon Regulatory Factor 1 | -1.589 | 8.63E-03 | -1.775 | 4.68E-11 | down | 0 | 0 | 0 |
| GREM1 | Gremlin 1, DAN Family BMP Antagonist | Inf | 4.60E-02 | 1.011 | 1.16E-08 | up | 0 | 0 | 0 |
SCLC, small cell lung cancer; circRNA, circular RNA; lncRNA, long noncoding RNA; miRNA, microRNA; mRNA, messenger RNA; ceRNA, competing endogenous RNA; FC, fold change; Inf, infinity; CLCGP, Clinical Lung Cancer Genome Project; U Cologne, University of Cologne study.