Skip to main content

Table 3 Gene ontology enrichment for the caudate nucleus network

From: A common gene expression signature in Huntington’s disease patient brain regions

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)  
  1. 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.