The KEGG pathway can be used for understanding high-level functions of genes and biological systems. We completed KEGG pathway analysis of the differentially expressed genes and the top 20 enriched KEGG pathways are shown in Fig. 4. Consistent with GO analysis, cell cycle and DNA replication were the most enriched KEGG pathways. Interestingly, cancer-related pathways, signaling pathways and adherens junction-related pathways were enriched in the differentially expressed genes of CD44+ cells. 
Figure 4.
KEGG pathway enrichment of differentially expressed genes The top right corner shows the most enriched KEGG pathways.
Table 4.
GO functional enrichment (biological process) of differentially expressed genes
| GO term | Number | Correlated P-value |
|---|---|---|
| G1/S transition of mitotic cell cycle (GO:0000082) | 104 | 1.49E-06 |
| Organ development (GO:0048513) | 226 | 1.63E-06 |
| Regulation of DNA-dependent DNA replication initiation (GO:0030174) | 20 | 3.84E-06 |
| DNA replication initiation (GO:0006270) | 39 | 1.51E-05 |
| Single-organism developmental process (GO:0044767) | 353 | 1.67E-05 |
| Chromosome segregation (GO:0007059) | 88 | 2.25E-05 |
| Cell division (GO:0051301) | 272 | 0.001320845 |
| DNA replication (GO:0006260) | 93 | 0.001664745 |
| Gene silencing (GO:0016458) | 29 | 0.001893301 |
| DNA strand elongation involved in DNA replication (GO:0006271) | 33 | 0.002818764 |
| Activation of protein kinase activity (GO:0032147) | 42 | 0.003097855 |
| Pyrimidine nucleoside salvage (GO:0043097) | 16 | 0.003181955 |
| Cell cycle process (GO:0022402) | 80 | 0.006871153 |
| Regulation of cell cycle (GO:0051726) | 109 | 0.007973628 |
| Cell cycle arrest (GO:0007050) | 108 | 0.008742882 |
| Negative regulation of transcription from RNA polymerase II promoter (GO:0000122) | 433 | 0.018076542 |
| Neurotrophin TRK receptor signaling pathway (GO:0048011) | 226 | 0.020824833 |
| Regulation of phosphorylation (GO:0042325) | 26 | 0.023171996 |
| Immune system process (GO:0002376) | 83 | 0.024763176 |
| G2/M transition of mitotic cell cycle (GO:0000086) | 127 | 0.028641706 |
| GO term | Number | Correlated P-value |
|---|---|---|
| G1/S transition of mitotic cell cycle (GO:0000082) | 104 | 1.49E-06 |
| Organ development (GO:0048513) | 226 | 1.63E-06 |
| Regulation of DNA-dependent DNA replication initiation (GO:0030174) | 20 | 3.84E-06 |
| DNA replication initiation (GO:0006270) | 39 | 1.51E-05 |
| Single-organism developmental process (GO:0044767) | 353 | 1.67E-05 |
| Chromosome segregation (GO:0007059) | 88 | 2.25E-05 |
| Cell division (GO:0051301) | 272 | 0.001320845 |
| DNA replication (GO:0006260) | 93 | 0.001664745 |
| Gene silencing (GO:0016458) | 29 | 0.001893301 |
| DNA strand elongation involved in DNA replication (GO:0006271) | 33 | 0.002818764 |
| Activation of protein kinase activity (GO:0032147) | 42 | 0.003097855 |
| Pyrimidine nucleoside salvage (GO:0043097) | 16 | 0.003181955 |
| Cell cycle process (GO:0022402) | 80 | 0.006871153 |
| Regulation of cell cycle (GO:0051726) | 109 | 0.007973628 |
| Cell cycle arrest (GO:0007050) | 108 | 0.008742882 |
| Negative regulation of transcription from RNA polymerase II promoter (GO:0000122) | 433 | 0.018076542 |
| Neurotrophin TRK receptor signaling pathway (GO:0048011) | 226 | 0.020824833 |
| Regulation of phosphorylation (GO:0042325) | 26 | 0.023171996 |
| Immune system process (GO:0002376) | 83 | 0.024763176 |
| G2/M transition of mitotic cell cycle (GO:0000086) | 127 | 0.028641706 |
Table 4.
GO functional enrichment (biological process) of differentially expressed genes
| GO term | Number | Correlated P-value |
|---|---|---|
| G1/S transition of mitotic cell cycle (GO:0000082) | 104 | 1.49E-06 |
| Organ development (GO:0048513) | 226 | 1.63E-06 |
| Regulation of DNA-dependent DNA replication initiation (GO:0030174) | 20 | 3.84E-06 |
| DNA replication initiation (GO:0006270) | 39 | 1.51E-05 |
| Single-organism developmental process (GO:0044767) | 353 | 1.67E-05 |
| Chromosome segregation (GO:0007059) | 88 | 2.25E-05 |
| Cell division (GO:0051301) | 272 | 0.001320845 |
| DNA replication (GO:0006260) | 93 | 0.001664745 |
| Gene silencing (GO:0016458) | 29 | 0.001893301 |
| DNA strand elongation involved in DNA replication (GO:0006271) | 33 | 0.002818764 |
| Activation of protein kinase activity (GO:0032147) | 42 | 0.003097855 |
| Pyrimidine nucleoside salvage (GO:0043097) | 16 | 0.003181955 |
| Cell cycle process (GO:0022402) | 80 | 0.006871153 |
| Regulation of cell cycle (GO:0051726) | 109 | 0.007973628 |
| Cell cycle arrest (GO:0007050) | 108 | 0.008742882 |
| Negative regulation of transcription from RNA polymerase II promoter (GO:0000122) | 433 | 0.018076542 |
| Neurotrophin TRK receptor signaling pathway (GO:0048011) | 226 | 0.020824833 |
| Regulation of phosphorylation (GO:0042325) | 26 | 0.023171996 |
| Immune system process (GO:0002376) | 83 | 0.024763176 |
| G2/M transition of mitotic cell cycle (GO:0000086) | 127 | 0.028641706 |
| GO term | Number | Correlated P-value |
|---|---|---|
| G1/S transition of mitotic cell cycle (GO:0000082) | 104 | 1.49E-06 |
| Organ development (GO:0048513) | 226 | 1.63E-06 |
| Regulation of DNA-dependent DNA replication initiation (GO:0030174) | 20 | 3.84E-06 |
| DNA replication initiation (GO:0006270) | 39 | 1.51E-05 |
| Single-organism developmental process (GO:0044767) | 353 | 1.67E-05 |
| Chromosome segregation (GO:0007059) | 88 | 2.25E-05 |
| Cell division (GO:0051301) | 272 | 0.001320845 |
| DNA replication (GO:0006260) | 93 | 0.001664745 |
| Gene silencing (GO:0016458) | 29 | 0.001893301 |
| DNA strand elongation involved in DNA replication (GO:0006271) | 33 | 0.002818764 |
| Activation of protein kinase activity (GO:0032147) | 42 | 0.003097855 |
| Pyrimidine nucleoside salvage (GO:0043097) | 16 | 0.003181955 |
| Cell cycle process (GO:0022402) | 80 | 0.006871153 |
| Regulation of cell cycle (GO:0051726) | 109 | 0.007973628 |
| Cell cycle arrest (GO:0007050) | 108 | 0.008742882 |
| Negative regulation of transcription from RNA polymerase II promoter (GO:0000122) | 433 | 0.018076542 |
| Neurotrophin TRK receptor signaling pathway (GO:0048011) | 226 | 0.020824833 |
| Regulation of phosphorylation (GO:0042325) | 26 | 0.023171996 |
| Immune system process (GO:0002376) | 83 | 0.024763176 |
| G2/M transition of mitotic cell cycle (GO:0000086) | 127 | 0.028641706 |
