Cluster analysis of differentially expressed genes. Red highlights genes with high expression, green shows cells with low expression and black indicates no significant change in the expression level between the mean and sample.
Protein-protein interaction network of differentially expressed genes. The red nodes represent upregulated genes and the green nodes represent downregulated genes. The lines represent the interaction between proteins.
Three subnetworks in the protein-protein interaction network of differentially expressed genes. (A) Subnetwork 1; (B) Subnetwork 2; and (C) Subnetwork 3 were determined. The red nodes represent upregulated genes and the green nodes represent downregulated genes. The lines represent the interaction relationship between proteins.
Top 10 most significantly up- or downregulated differentially expressed genes in triple-negative breast cancer compared with normal tissue.
| Gene symbol | P-value | Fold-change |
|---|---|---|
| Upregulated genes | ||
| BIRC5 | 6.50×10−36 | 48.63 |
| MYBL2 | 4.32×10−34 | 57.33 |
| TOP2A | 3.49×10−31 | 41.91 |
| CDC2 | 4.07×10−29 | 32.75 |
| MMP9 | 2.09×10−23 | 21.35 |
| CHEK1 | 8.68×10−23 | 13.37 |
| SPP1 | 2.21×10−22 | 40.41 |
| TYMS | 4.26×10−22 | 18.21 |
| E2F1 | 4.38×10−21 | 11.18 |
| PCNA | 1.27×10−20 | 6.87 |
| Downregulated genes | ||
| IGFBP6 | 2.19×10−14 | 0.12 |
| ESR1 | 1.09×10−13 | 0.09 |
| DLC1 | 1.27×10−12 | 0.14 |
| EGR1 | 6.87×10−11 | 0.20 |
| IGF1 | 1.72×10−10 | 0.27 |
| TGFBR3 | 3.37×10−10 | 0.16 |
| PPARG | 3.84×10−10 | 0.23 |
| NGFR | 3.93×10−10 | 0.12 |
| CD34 | 6.67×10−9 | 0.27 |
| FOS | 5.83×10−8 | 0.30 |
Top five significantly enriched biology processes for differentially expressed genes.
| GO ID | Term | Gene counts | P-value | FDR |
|---|---|---|---|---|
| Upregulated | ||||
| GO:0042127 | Regulation of cell proliferation | 35 | 2.22×10−18 | 3.76×10−15 |
| GO:0051726 | Regulation of cell cycle | 24 | 8.20×10−17 | 1.89×10−13 |
| GO:0008284 | Positive regulation of cell proliferation | 26 | 8.35×10−17 | 1.89×10−13 |
| GO:0042981 | Regulation of apoptosis | 31 | 2.15×10−14 | 3.63×10−11 |
| GO:0043067 | Regulation of programmed cell death | 31 | 2.79×10−14 | 4.72×10−11 |
| Downregulated | ||||
| GO:0042127 | Regulation of cell proliferation | 12 | 1.19×10−9 | 1.88×10−6 |
| GO:0010604 | Positive regulation of macromolecule metabolic process | 11 | 5.40×10−8 | 8.57×10−5 |
| GO:0030334 | Regulation of cell migration | 7 | 8.25×10−8 | 1.31×10−4 |
| GO:0040012 | Regulation of locomotion | 7 | 1.76×10−7 | 2.79×10−4 |
| GO:0051270 | Regulation of cell motion | 7 | 1.81×10−7 | 2.88×10−4 |
GO, gene ontology; Gene counts, number of genes; FDR, false discovery rate.
Significantly enriched pathways for differentially expressed genes.
| KEGG ID | Term | Gene counts | P-value | FDR |
|---|---|---|---|---|
| hsa05200 | Pathways in cancer | 37 | 3.77×10−24 | 4.19×10−21 |
| hsa05219 | Bladder cancer | 17 | 8.90×10−20 | 9.87×10−17 |
| hsa05223 | Non-small cell lung cancer | 14 | 3.04×10−13 | 3.38×10−10 |
| hsa04110 | Cell cycle | 18 | 1.03×10−12 | 1.14×10−9 |
| hsa05215 | Prostate cancer | 16 | 1.05×10−12 | 1.16×10−9 |
| hsa05212 | Pancreatic cancer | 14 | 1.59×10−11 | 1.76×10−8 |
| hsa05220 | Chronic myeloid leukemia | 14 | 2.74×10−11 | 3.04×10−8 |
| hsa05214 | Glioma | 13 | 5.32×10−11 | 5.91×10−8 |
| hsa05218 | Melanoma | 13 | 2.33×10−10 | 2.59×10−7 |
| hsa05213 | Endometrial cancer | 11 | 2.22×10−9 | 2.46×10−6 |
| hsa05222 | Small cell lung cancer | 12 | 2.30×10−8 | 2.56×10−5 |
| hsa05216 | Thyroid cancer | 8 | 1.25×10−7 | 1.39×10−4 |
| hsa05210 | Colorectal cancer | 10 | 2.74×10−6 | 3.04×10−3 |
| hsa04115 | p53 signaling pathway | 9 | 5.03×10−6 | 5.58×10−3 |
KEGG, Kyoto Encyclopedia of Genes and Genomes; Gene counts, number of genes; FDR, false discovery rate.
Top five significantly enriched biology processes for differentially expressed genes in three subnetworks.
| GO ID | Term | Gene counts | P-value | FDR |
|---|---|---|---|---|
| Subnetwork 1 | ||||
| GO:0042127 | Regulation of cell proliferation | 30 | 3.15×10−20 | 5.31×10−17 |
| GO:0010647 | Positive regulation of cell communication | 21 | 7.11×10−18 | 1.20×10−14 |
| GO:0009967 | Positive regulation of signal transduction | 20 | 1.89×10−17 | 3.19×10−14 |
| GO:0008284 | Positive regulation of cell proliferation | 22 | 3.59×10−17 | 6.06×10−14 |
| GO:0009719 | Response to endogenous stimulus | 21 | 4.01×10−16 | 7.44×10−13 |
| Subnetwork 2 | ||||
| GO:0022402 | Cell cycle process | 24 | 1.05×10−20 | 1.65×10−17 |
| GO:0007049 | Cell cycle | 26 | 3.03×10−20 | 4.79×10−17 |
| GO:0051726 | Regulation of cell cycle | 19 | 3.49×10−18 | 5.51×10−15 |
| GO:0022403 | Cell cycle phase | 20 | 7.57×10−18 | 1.20×10−14 |
| GO:0051329 | Interphase of mitotic cell cycle | 13 | 3.33×10−16 | 5.22×10−13 |
| Subnetwork 3 | ||||
| GO:0022402 | Cell cycle process | 23 | 1.66×10−20 | 2.59×10−17 |
| GO:0007049 | Cell cycle | 25 | 2.88×10−20 | 4.51×10−17 |
| GO:0051726 | Regulation of cell cycle | 19 | 4.22×10−19 | 6.61×10−16 |
| GO:0022403 | Cell cycle phase | 19 | 2.27×10−17 | 3.55×10−14 |
| GO:0006259 | DNA metabolic process | 20 | 3.35×10−17 | 5.25×10−14 |
GO, gene ontology; Gene counts, number of genes; FDR, false discovery rate.
Top five significantly enriched pathways for differentially expressed genes in three subnetworks.
| KEGG ID | Term | Gene counts | P-value | FDR |
|---|---|---|---|---|
| Subnetwork 1 | ||||
| hsa05200 | Pathways in cancer | 32 | 3.04×10−25 | 3.30×10−22 |
| hsa05219 | Bladder cancer | 15 | 4.66×10−19 | 5.05×10−16 |
| hsa05215 | Prostate cancer | 14 | 1.23×10−12 | 1.34×10−9 |
| hsa05213 | Endometrial cancer | 11 | 3.80×10−11 | 4.12×10−8 |
| hsa05218 | Melanoma | 12 | 4.29×10−11 | 4.65×10−8 |
| Subnetwork 2 | ||||
| hsa04110 | Cell cycle | 19 | 3.60×10−20 | 3.72×10−17 |
| hsa05200 | Pathways in cancer | 21 | 5.11×10−15 | 5.27×10−12 |
| hsa05215 | Prostate cancer | 11 | 3.82×10−10 | 3.94×10−7 |
| hsa04115 | p53 signaling pathway | 10 | 7.34×10−10 | 7.57×10−7 |
| hsa05220 | Chronic myeloid leukemia | 10 | 1.81×10−9 | 1.86×10−6 |
| Subnetwork 3 | ||||
| hsa04110 | Cell cycle | 18 | 2.32×10−19 | 2.37×10−16 |
| hsa05200 | Pathways in cancer | 19 | 2.03×10−13 | 2.07×10−10 |
| hsa04115 | p53 signaling pathway | 9 | 9.25×10−9 | 9.43×10−6 |
| hsa05220 | Chronic myeloid leukemia | 9 | 2.04×10−8 | 2.08×10−5 |
| hsa05223 | Non-small cell lung cancer | 8 | 4.40×10−8 | 4.49×10−5 |
KEGG, Kyoto Encyclopedia of Genes and Genomes; Gene counts, number of genes; FDR, false discovery rate.