Table 2.
Gene ontology analysis of MeCP2 bound promoters
| 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 |
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]