Table 3 Enrichment clustering of the differentially methylated genesa
Term | Gene count | % of the total genes entered | Genes in each pathway from our result | Fold Enrichment | Bonferroni P-value |
|---|---|---|---|---|---|
GO:0048705 ~ skeletal system morphogenesis | 14 | 9.6 | GSC, TBX15, PAX1, GLI3, HOXB3, HOXD9, HOXC8, HOXD8, HOXC9, OSR2, HOXD3, HOXB6, ALX4, RUNX2 | 14.96 | 8.39E-09 |
GO:0048704 ~ embryonic skeletal system morphogenesis | 10 | 6.9 | HOXD9, HOXB3, GSC, OSR2, TBX15, HOXC9, HOXD3, HOXB6, ALX4, GLI3 | 21.00 | 9.89E-07 |
GO:0001501 ~ skeletal system development | 17 | 11.7 | CYP24A1, GSC, TBX15, GLI3, PAX1, GLI1, HOXD9, HOXB3, HDAC4, HOXC8, HOXD8, HOXC9, OSR2, HOXD3, HOXB6, ALX4, RUNX2 | 6.38 | 8.98E-06 |
GO:0048562 ~ embryonic organ morphogenesis | 12 | 8.3 | HOXD9, HOXB3, GSC, OSR2, TBX15, HOXC9, HOXD3, HOXB6, VAX2, ALX4, GLI3, GLI1 | 10.80 | 1.43E-05 |
GO:0048706 ~ embryonic skeletal system development | 10 | 6.8 | HOXD9, HOXB3, GSC, OSR2, TBX15, HOXC9, HOXD3, HOXB6, ALX4, GLI3 | 15.54 | 1.55E-05 |
GO:0003002 ~ regionalization | 13 | 8.9 | GSC, VAX2, PAX1, GLI3, GLI1, HOXB3, HOXD9, HOXC8, HOXC9, HOXD8, HOXD3, HOXB6, ALX4 | 7.91 | 9.34E-05 |
GO:0043565 ~ sequence-specific DNA bindingb | 20 | 13.8 | GSC, ESRRG, VAX2, MEIS1, GLI3, GLI1, HOXD9, HOXB3, HDAC4, HOXC8, HOXD8, MEIS2, HOXC9, HAND2, GATA6, HOXD3, HOXB6, THAP1, ALX4, ETV6 | 4.03 | 1.02E-04 |
GO:0048568 ~ embryonic organ development | 12 | 8.3 | HOXD9, HOXB3, GSC, OSR2, TBX15, HOXC9, HOXD3, HOXB6, VAX2, ALX4, GLI3, GLI1 | 8.35 | 2.05E-04 |
Homeoboxb | 12 | 8.3 | HOXD9, HOXB3, HOXC8, GSC, HOXD8, MEIS2, HOXC9, HOXD3, HOXB6, VAX2, ALX4, MEIS1 | 6.96 | 3.14E-04 |
GO:0007389 ~ pattern specification process | 14 | 9.6 | GSC, VAX2, PAX1, GLI3, GLI1, HOXB3, SEMA5A, HOXD9, HOXC8, HOXD8, HOXC9, HOXD3, HOXB6, ALX4 | 6.27 | 3.57E-04 |
SM00389:HOXb | 12 | 8.3 | HOXD9, HOXB3, HOXC8, GSC, HOXD8, MEIS2, HOXC9, HOXD3, HOXB6, VAX2, ALX4, MEIS1 | 5.65 | 5.84E-04 |
IPR017970:Homeobox, conserved siteb | 12 | 8.3 | HOXD9, HOXB3, HOXC8, GSC, HOXD8, MEIS2, HOXC9, HOXD3, HOXB6, VAX2, ALX4, MEIS1 | 6.62 | 6.07E-04 |
IPR001356:Homeoboxb | 12 | 8.3 | HOXD9, HOXB3, HOXC8, GSC, HOXD8, MEIS2, HOXC9, HOXD3, HOXB6, VAX2, ALX4, MEIS1 | 6.54 | 6.87E-04 |
IPR012287:Homeodomain-relatedb | 12 | 8.3 | HOXD9, HOXB3, HOXC8, GSC, HOXD8, MEIS2, HOXC9, HOXD3, HOXB6, VAX2, ALX4, MEIS1 | 6.46 | 7.77E-04 |
GO:0009952 ~ anterior/posterior pattern formationb | 10 | 6.9 | HOXD9, HOXB3, HOXC8, HOXD8, HOXC9, HOXD3, HOXB6, ALX4, PAX1, GLI3 | 8.55 | 0.002 |
DNA-binding region:Homeoboxb | 10 | 6.9 | HOXD9, HOXB3, HOXC8, GSC, HOXD8, HOXC9, HOXD3, HOXB6, VAX2, ALX4 | 7.34 | 0.004 |
IPR001827:Homeobox protein, antennapedia type, conserved siteb | 5 | 3.4 | HOXB3, HOXC8, HOXD8, HOXD3, HOXB6 | 26.69 | 0.01 |
GO:0043009 ~ chordate embryonic developmentb | 13 | 8.9 | GSC, TBX15, PAX1, GLI3, HOXB3, HOXD9, HOXC9, OSR2, HAND2, GATA6, HOXD3, HOXB6, ALX4 | 4.70 | 0.02 |
GO:0009792 ~ embryonic development ending in birth or egg hatchingb | 13 | 8.9 | GSC, TBX15, PAX1, GLI3, HOXB3, HOXD9, HOXC9, OSR2, HAND2, GATA6, HOXD3, HOXB6, ALX4 | 4.66 | 0.02 |
GO:0003700 ~ transcription factor activityb | 21 | 14.5 | TBX15, GSC, ESRRG, VAX2, MEIS1, GLI3, GLI1, HOXD9, HOXB3, HOXC8, HOXD8, MEIS2, HOXC9, HAND2, GATA6, HOXD3, MLLT10, HOXB6, ALX4, ETV6, RUNX2 | 2.64 | 0.02 |
Developmental proteinb | 17 | 11.7 | GSC, ZNF521, VAX2, MEIS1, PAX1, GLI1, HOXD9, HOXB3, SEMA5A, HOXC8, HOXD8, HOXC9, HAND2, HOXD3, HOXB6, ROBO2, ALX4 | 3.06 | 0.03 |