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Table 3 Summary of the ORA

From: A genome-wide DNA methylation signature for SETD1B-related syndrome

Gene ontology: biological processes
  Description C O E R pValue FDR
GO:0051276 Chromosome organization 1143 165 97.67 1.69 5.59E−12 5.08E−08
GO:0033043 Regulation of organelle organization 1245 175 106.39 1.64 1.16E−11 5.26E−08
GO:0007049 Cell cycle 1739 223 148.60 1.50 1.15E−10 3.48E−07
GO:0006915 Apoptotic process 1911 239 163.30 1.46 2.52E−10 5.74E−07
GO:0010941 Regulation of cell death 1648 210 140.83 1.49 7.83E−10 1.42E−06
GO:0006325 Chromatin organization 741 112 63.32 1.77 1.35E−09 1.90E−06
GO:0033554 Cellular response to stress 1867 231 159.54 1.45 1.47E−09 1.90E−06
GO:0010942 Positive regulation of cell death 660 102 56.40 1.81 2.28E−09 2.60E−06
GO:0010629 Negative regulation of gene expression 1733 216 148.09 1.46 3.00E−09 2.87E−06
GO:0034613 Cellular protein localization 1815 224 155.10 1.44 3.44E−09 2.87E−06
Gene ontology: molecular function
 GO:0003723 RNA binding 1603 203 131.47 1.54 7.52E−11 8.28E−08
 GO:0019904 Protein domain specific binding 684 106 56.10 1.89 8.82E−11 8.28E−08
 GO:0001067 Regulatory region nucleic acid binding 898 129 73.65 1.75 1.39E−10 8.70E−08
 GO:0044212 Transcription regulatory region DNA binding 896 128 73.48 1.74 2.38E−10 1.12E−07
 GO:0043565 Sequence-specific DNA binding 1097 146 89.97 1.62 1.87E−09 7.02E−07
 GO:0003690 Double-stranded DNA binding 915 126 75.04 1.68 3.41E−09 1.07E−06
 GO:0000976 Transcription regulatory region sequence-specific DNA binding 781 111 64.05 1.73 5.41E−09 1.45E−06
 GO:1990837 Sequence-specific double-stranded DNA binding 823 115 67.50 1.70 7.55E−09 1.77E−06
 GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding 729 103 59.79 1.72 2.69E−08 5.62E−06
 GO:0001012 RNA polymerase II regulatory region DNA binding 735 103 60.28 1.71 4.11E−08 7.72E−06
Human Phenotype Ontology
 HP:0002346 Head tremor 20 10 1.87 5.36 3.48E−06 0.016253
 HP:0011337 Abnormality of mouth size 269 43 25.09 1.71 2.13E−04 0.167774
 HP:0004097 Deviation of finger 320 49 29.85 1.64 2.23E−04 0.167774
 HP:0000311 Round face 73 17 6.81 2.50 2.80E−04 0.167774
 HP:0000219 Thin upper lip vermilion 137 26 12.78 2.03 2.84E−04 0.167774
 HP:0011228 Horizontal eyebrow 8 5 0.75 6.70 3.04E−04 0.167774
 HP:0005306 Capillary hemangioma 26 9 2.43 3.71 3.59E−04 0.167774
 HP:0001894 Thrombocytosis 21 8 1.96 4.08 3.63E−04 0.167774
 HP:0100559 Lower limb asymmetry 21 8 1.96 4.08 3.63E−04 0.167774
 HP:0000107 Renal cyst 203 34 18.93 1.80 4.21E−04 0.167774
  1. C reference genes in the category, O observed number of genes in the category, E expected number of genes in the category, R ratio of enrichment, pValue p value from hypergeometric test, FDR false discovery rate