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Table 2 Gene ontology analysis of MeCP2 bound promoters

From: Genome-wide redistribution of MeCP2 in dorsal root ganglia after peripheral nerve injury

GO term p value q value FDR B&H Hit count in query list GO accession
Molecular function
 RNA polymerase II transcription factor activity, sequence-specific DNA binding 2.09E−09 6.41E−06 214 GO:0000981
 Transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 7.30E−08 1.12E−04 125 GO:0001228
 Transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 1.13E−07 1.16E−04 126 GO:0000982
 Enzyme binding 3.44E−06 2.12E−03 500 GO:0019899
 Regulatory region DNA binding 3.82E−06 2.12E−03 247 GO:0000975
 Transcription regulatory region DNA binding 4.16E−06 2.12E−03 246 GO:0044212
 Regulatory region nucleic acid binding 5.08E−06 2.23E−03 247 GO:0001067
 Receptor binding 1.94E−05 5.74E−03 427 GO:0005102
 Sequence-specific double-stranded DNA binding 2.10E−05 5.74E−03 211 GO:1990837
 Double-stranded DNA binding 2.15E−05 5.74E−03 233 GO:0003690
Biological process
 Tissue development 7.05E−18 7.67E−14 595 GO:0009888
 Skeletal system development 5.71E−17 3.11E−13 203 GO:0001501
 Organ morphogenesis 9.09E−16 3.30E−12 345 GO:0009887
 Regulation of multicellular organismal 3.00E−15 7.71E−12 541 GO:2000026
 Regulation of cell differentiation 3.54E−15 7.71E−12 509 GO:0045595
 Regulation of nervous system development 6.60E−15 1.20E−11 292 GO:0051960
 Neurogenesis 8.78E−15 1.37E−11 557 GO:0022008
 Regulation of cell development 4.71E−14 6.42E−11 316 GO:0060284
 Generation of neurons 1.11E−13 1.34E−10 528 GO:0048699
 Positive regulation of cell differentiation 3.12E−13 3.28E−10 309 GO:0045597
Cellular component
 Neuron projection 2.19E−08 2.77E−05 333 GO:0043005
 Neuron part 1.99E−07 1.26E−04 409 GO:0097458
 Somatodendritic compartment 1.93E−06 8.17E−04 246 GO:0036477
 Cell body 8.24E−06 1.86E−03 197 GO:0044297
 Integral component of plasma membrane 8.41E−06 1.86E−03 427 GO:0005887
 Neuronal cell body 8.81E−06 1.86E−03 178 GO:0043025
 Anchoring junction 1.21E−05 2.19E−03 152 GO:0070161
 Intrinsic component of plasma membrane 1.66E−05 2.63E−03 440 GO:0031226
 Potassium channel complex 2.10E−05 2.96E−03 38 GO:0034705
 Adherens junction 3.00E−05 3.80E−03 145 GO:0005912
  1. The top ten enriched gene ontology (GO) terms with p < 0.01 are listed for molecular function, biological process, and cellular component, respectively. GO analysis of our ChIP-seq results indicates that MeCP2 binding occurs at the promoter of genes with neuronal function, ion channel activity and cellular membrane functions. These results closely correspond with previous reports of genes repressed by MeCP2 in brain [16]