Bioinformatic Analysis for Influential Core Gene Identification and Prognostic Significance in Advanced Serous Ovarian Carcinoma
Abstract
:1. Introduction
2. Materials and Methods
2.1. Microarray Data Source and Cluster Analysis
2.2. Screening for DEGs
2.3. GO Analysis of DEGs
2.4. PPI Network Analysis
2.5. DEG Survival Analysis
2.6. Data Source for Analysis of Association with Clinicopathological Parameters
2.7. Statistical Analysis
3. Results
3.1. DEG Identification
3.2. Expression of the Identified DEGs between Normal and Serous Ovarian Cancer Tissues
3.3. PPI Network Construction
3.4. Clustered Genes Are Mainly Involved in Cell Cycle Regulation
3.5. Higher Expression of CDCA3 and UBE2C Associated with Poor OS in All Stages
3.6. Higher CDCA3 and UBE2C Expression Associated with Higher Histologic Grades
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Platform | GEO Dataset | Samples | Reference |
---|---|---|---|
GPL570 | GSE14407 | 12 Normal, 12 Cancer | Bowen et al. [13] |
GPL570 | GSE36668 | 4 Normal, 4 Cancer | Elgaaen et al. [14] |
GPL570 | GSE38666 | 12 Normal, 18 Cancer | Lili et al. [15] |
Gene Names | Log2FC | Adjusted p-Value | ||||
---|---|---|---|---|---|---|
GSE14407 | GSE36668 | GSE38666 | GSE14407 | GSE36668 | GSE38666 | |
BIRC5 | 3.784515 | 13.83283 | 3.792818 | 4.58 × 10−6 | 2.45 × 10−4 | 3.34 × 10−8 |
CDCA3 | 3.40002 | 3.542135 | 3.543772 | 9.12 × 10−7 | 2.72 × 10−3 | 2.20 × 10−9 |
CENPF | 3.904451 | 3.450972 | 3.934447 | 1.69 × 10−7 | 3.17 × 10−3 | 2.20 × 10−9 |
KIF4A | 3.533572 | 5.173891 | 3.746773 | 4.76 × 10−6 | 2.84 × 10−3 | 1.70 × 10−8 |
NCAPG | 3.233566 | 3.533272 | 3.092676 | 5.15 × 10−6 | 3.17 × 10−3 | 1.26 × 10−7 |
RRM2 | 3.212708 | 4.504844 | 3.215252 | 3.24 × 10−6 | 3.17 × 10−3 | 2.23 × 10−8 |
UBE2C | 2.539233 | 3.816594 | 2.699924 | 7.37 × 10−6 | 2.56 × 10−3 | 1.26 × 10−7 |
VEGFA | 2.86746 | 2.906894 | 2.647287 | 2.89 × 10−6 | 2.84 × 10−3 | 4.33 × 10−7 |
NR2F6 | 2.950696 | 2.75339 | 3.029833 | 1.85 × 10−5 | 2.72 × 10−3 | 1.63 × 10−7 |
Gene Names | Log2FC | Adjusted p-Value | ||||
---|---|---|---|---|---|---|
GSE14407 | GSE36668 | GSE38666 | GSE14407 | GSE36668 | GSE38666 | |
C21orf62 | −3.784515 | −13.83283 | −3.792818 | 4.58 × 10−6 | 2.45 × 10−4 | 3.34 × 10−8 |
MUM1L1 | −3.40002 | −3.542135 | −3.543772 | 9.12 × 10−7 | 2.72 × 10−3 | 2.20 × 10−9 |
NBEA | −3.904451 | −3.450972 | −3.934447 | 1.69 × 10−7 | 3.17 × 10−3 | 2.20 × 10−9 |
RNASE4 | −3.533572 | −5.173891 | −3.746773 | 4.76 × 10−6 | 2.84 × 10−3 | 1.70 × 10−8 |
RORA | −3.233566 | −3.533272 | −3.092676 | 5.15 × 10−6 | 3.17 × 10−3 | 1.26 × 10−7 |
LOC101930363 /LOC101928349 /LOC100507387 /FAM153C /FAM153A /FAM153B | −4.26894 | −3.17681 | −4.17039 | 4.56 × 10−7 | 0.003168 | 8.62 × 10−9 |
Gene Names | Fold Change | p-Value |
---|---|---|
BIRC5 | 157.01 | 1.09 × 10−65 |
CDCA3 | 2.58 | 1.7 × 10−29 |
CENPF | 18.82 | 1.23 × 10−63 |
KIF4A | 34.68 | 2.54 × 10−64 |
NCAPG | 29.63 | 5.23 × 10−64 |
NR2F6 | 11.6 | 4.15 × 10−65 |
RRM2 | 41.23 | 2.99 × 10−64 |
UBE2C | 101.05 | 3.88 × 10−65 |
VEGFA | 2.61 | 3.13 × 10−34 |
Gene Names | Fold Change | p-Value |
---|---|---|
C21orf62 | 0.02 | 8.79 × 10−63 |
MUM1L1(PWWP3B) | 0.01 | 5.22 × 10−65 |
NBEA | 0.11 | 2.62 × 10−64 |
RNASE4 | 0.01 | 6.84 × 10−66 |
RORA | 0.15 | 4.99 × 10−63 |
Category | Term | Gene Names | p-Value |
---|---|---|---|
GO_BP | GO:0051301 Cell division | BIRC5, CDCA3, CENPF, NCAPG, UBE2C | 5.5 × 10−5 |
GO:0031536 Positive regulation of exit from mitosis | BIRC5, UBE2C | 3.9 × 10−3 | |
GO:0000278 Mitotic nuclear division | BIRC5, CDCA3, CENPF | 1.1 × 10−2 | |
GO:0016567 Protein ubiquitination | BIRC5, CDCA3, UBE2C | 2.2 × 10−2 | |
GO:0030522 Intracellular receptor signaling pathway | RORA, NR2F6 | 2.5 × 10−2 | |
GO:0043401 Steroid hormone mediated signaling pathway | RORA, NR2F6 | 3.7 × 10−2 | |
GO:0043154 Negative regulation of cysteine–type endopeptidase activity involved in apoptotic process | BIRC5, VEGFA | 4.4 × 10−2 | |
GO_CC | Cytosol | BIRC5, CDCA3, CENPF, KIF4A, NBEA, NCAPG, RRM2, UBE2C | 2.2 × 10−3 |
Midbody | BIRC5, CENPF, KIF4A | 3.1 × 10−3 | |
Nucleoplasm | RORA, BIRC5, CENPF, KIF4A, NR2F6, RRM2, UBE2C | 5.1 × 10−3 | |
Spindle microtubule | BIRC5, KIF4A | 2.9 × 10−2 | |
Chromosome, centromeric region | BIRC5, CENPF | 3.7 × 10−2 | |
GO_MF | RNA polymerase II transcription factor activity, ligand activated sequence–specific DNA | RORA, NR2F6 | 2.3 × 10−2 |
Steroid hormone receptor activity | RORA, NR2F6 | 3.6 × 10−2 | |
Protein binding | RORA, BIRC5, CDCA3, CENPF, KIF4A, NCAPG, NR2F6, RRM2, UBE2C, VEGFA | 4.4 × 10−2 |
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Song, C.; Kim, K.-B.; Lee, J.-H.; Kim, S. Bioinformatic Analysis for Influential Core Gene Identification and Prognostic Significance in Advanced Serous Ovarian Carcinoma. Medicina 2021, 57, 933. https://doi.org/10.3390/medicina57090933
Song C, Kim K-B, Lee J-H, Kim S. Bioinformatic Analysis for Influential Core Gene Identification and Prognostic Significance in Advanced Serous Ovarian Carcinoma. Medicina. 2021; 57(9):933. https://doi.org/10.3390/medicina57090933
Chicago/Turabian StyleSong, Changho, Kyoung-Bo Kim, Jae-Ho Lee, and Shin Kim. 2021. "Bioinformatic Analysis for Influential Core Gene Identification and Prognostic Significance in Advanced Serous Ovarian Carcinoma" Medicina 57, no. 9: 933. https://doi.org/10.3390/medicina57090933