Table 3.
Gene ontology enrichment for the caudate nucleus network
| Module | cor | GO-term (DAVID) | Potential regulators |
|---|---|---|---|
| CNpos1 | up | regulation of transcription (6.18, 0.000) | YY1 (0.000)2, ELK1 (0.001)2, GABPB1 (0.002)2, SP1 (0.002)2, NRF1 (0.002)2, E2F (0.007)2, IRF1 (0.011)2, GTF3A (0.032)2, SOX9 (0.033)2 |
| chromatin modification (3.85, 0.003) | |||
| mRNA processing (3.71, 0.004) | |||
| CNpos2 | up | regulation of transcription (5.94, 0.001) | NFAT (0.004)2 |
| cell migration (4.09, 0.004) | |||
| lipid metabolism (2.51, 0.001) | |||
| CNpos3 | up | RNA binding (0.65, 1.0) | |
| CNpos4 | up | chromatin organization (2.45, 0.008) | EGR2 (0.010)2, MYC (0.040)2, TCF3 (0.040)2, NR2F2 (0.040)2, TCF12 (0.040)2, SP1 (0.040)2, EGR1 (0.040)2, EGR4 (0.040)2 |
| CNpos5 | up | cilium (2.79, 0.003) | |
| CNpos6 | up | inflammatory response (8.33, 0.000) | STAT5A (0.000)2, STAT3 (0.000)2, STAT5B (0.000)2, BACH2 (0.002)2, NFAT (0.005)2, JUN (0.020)2, NFE2 (0.035)2 |
| CNpos7 | up | regulation of transcription (3.0, 0.045) | |
| CNpos8 | up | inflammatory response (14.15, 0.000) | ELF1 (0.000)2, STAT1/STAT2 (0.017)2, IRF1 (0.017)2 |
| icosanoid metabolism (1.73, 0.001) | |||
| CNpos9 | up | myelination (3.06, 0.002) | |
| oligodendrocyte/glial differentiation (2.4, 0.054) | |||
| CNneg1 | down | synapse (12.23, 0.000) | miR16 (0.018)1, NRF1 (0.03)1
REST (0.000)2, EGR1 (0.000)2, SF1 (0.000)2, CREB1 (0.000)2, JUN (0.000)2, EGR4 (0.000)2, MYOD1 (0.000)2, TCF3 (0.000)2, RORA (0.000)2, ATF1 (0.000)2, E4F1 (0.000)2, SP1 (0.000)2, ESRRA (0.001)2, TCF11 (0.002)2, PAX4 (0.002)2, TFAP4 (0.003)2, MAZ (0.003)2, HAND1 (0.006)2, EGR2 (0.007)2, NRF2 (0.007)2, ATF3 (0.008)2, RFX1 (0.008)2, POU3F1 (0.008)2, LEF1 (0.011)2, POU1F1 (0.019)2, MYB (0.027)2, TCF12 (0.041)2, NFE2 (0.041)2, MEIS1 (0.044)2, SREBF1 (0.050)2 |
| ion channels (4.61, 0.000) | |||
| regulation of synaptic plasticity (4.58, 0.000) | |||
| protein transport (2.89, 0.011) | |||
| protein targeting to mitochondrion (2.75, 0.007) | |||
| CNneg2 | down | mitochondrion (20.31, 0.000) | YY1 (0.005)1, ETS1 (0.005)1, NRF1 (0.005)1
ELK1 (0.000)2 |
| proteasome/protein catabolic process (5.83, 0.000) | |||
| mitochondrial ribosome (4.54, 0.000) | |||
| chaperones (3.17, 0.012) | |||
| spliceosome (3.0, 0.002) | |||
| DNA repair (2.47, 0.027) | |||
| translation initiation (1.95, 0.007) | |||
| CNneg3 | down | hemoglobin complex (1.74, 0.024) | |
| HTT | down | neuron projection (1.93, 0.56) |
Gene ontology (GO) enrichment for the caudate nucleus network. Genes in the identified modules were analyzed using DAVID. The sign of the correlation (cor) with HD and the over-represented GO-terms are shown. The first number in brackets after the GO-term is the respective fold enrichment, the second number the adjusted P-value, as determined by DAVID. All significantly enriched (adjusted P <0.05) GO-terms are shown. In cases where no significantly enriched GO-term was identified, the GO-term with the highest fold enrichment is shown. Potential regulators of a module were identified using 1GO-Elite, or 2WebGestalt. Adjusted P-values are given in brackets after the name. Regulators that were identified by both tools are highlighted in bold. HTT is part of the CNneg1 module in the caudate nucleus network. The GO-term enrichment for 100 genes with the highest correlation with HTT is shown.