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Table 3 Enrichment clustering of the differentially methylated genesa

From: Genome-wide DNA methylation study of hip and knee cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis

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
  1. aAll of the GO terms above were clustered into one annotation cluster with an overall enrichment score of 3.95. bThe GO terms were only significant before the removal of the genes differentially methylated between hip OA and knee OA
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