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Table 6 Gene ontology enrichment for the consensus networks in human datasets

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

Module cor GO-term (DAVID) Potential regulators
Parkinson’s disease (PD)
PDpos1 up IκB kinase/NFκB (3.59, 0.032)  
PDpos2 up lipid synthesis (2, 0.01)  
PDneg1 down synapse (5.87, 0.000) miR16 (0.036)1
mitochondrion (4.6, 0.000) ESRRA (0.001)2, SF1 (0.003)2
calmodulin binding (3.12, 0.044)
Myotonic dystrophy type 1 (DM1)
DM1pos1 up regulation of neurogenesis (1.55, 0.99) MEF2 (0.040)2, E2F (0.040)2, NR3C1 (0.040)2, PITX2 (0.040)2, ATF6 (0.040)2, VDR (0.040)2, ATF1 (0.040)2, TP53 (0.041)2
DM1neg1 down axon (1.18, 0.98) POU2F1 (0.011)2, POU1F1 (0.034)2, IRF2 (0.048)2
DM1neg2 down enzyme activator activity (2.52, 0.049)  
DM1neg3 down synapse (2.29, 0.008) SF1 (0.001)2, REST (0.032)2
Myotonic dystrophy type 2 (DM2)
DM2pos1 up lysosome (3.03, 0.043)  
DM2pos2 up regulation of transcription (1.51, 0.99)  
DM2pos3 up tubulin binding (1.64, 0.52)  
DM2pos4 up sarcomer (1, 1.0)  
DM2neg1 down mitochondrion (3.09, 0.01)  
DM2neg2 down dendrite (1.91, 0.51) NRF1 (0.009)1, ETS1 (0.054)1
Ganglioglioma (GG)
GGpos1 up inflammatory response (6.32, 0.002) NFκB (0.022)1, miR124 (0.022)1, miR106b (0.022)1, MYOG (0.066)1
cell adhesion/extracellular matrix (4.13, 0.002) ELF1 (0.000)2, IRF8 (0.008)2, MYB (0.008)2, ELK1 (0.010)2, SPI1 (0.010)2, CEBPA (0.016)2, NFAT (0.029)2, IRF1 (0.034)2, STAT5A (0.034)2, AHR (0.043)2, SOX5 (0.049)2, TP53 (0.049)2
GGneg1 down axon (11.88, 0.000) REST (0.000)2, SF1 (0.000)2, TCF3 (0.000)2, ESRRA (0.000)2, MYOD (0.000)2, RFX1 (0.000)2, RORA (0.000)2, EGR1 (0.000)2, JUN (0.000)2, TCF11 (0.000)2, ATF3 (0.000)2, LEF1 (0.000)2, PAX4 (0.000)2, E4F1 (0.000)2, CREB (0.000)2, HLF (0.001)2, MAZ (0.001)2, SP1 (0.001)2, NFIL3 (0.001)2, BACH1 (0.002)2, ATF2 (0.002)2, ATF1 (0.002)2, TFAP4 (0.002)2, TCF8 (0.003)2, ZNF238 (0.004)2, NFE2 (0.005)2, HSF1 (0.006)2, MIF (0.010)2, CUTL1 (0.012)2, SREBF1 (0.016)2, NF1 (0.020)2, MEIS1 (0.020)2, HSF2 (0.021)2, NFE2L2 (0.021)2, PCAF (0.023)2, GCF1 (0.034)2, ITGAL (0.034)2, ATF4 (0.035)2, MAF (0.038)2, TAL1 (0.043)2, NR1H4 (0.044)2, GATA2 (0.044)2, SOX9 (0.046)2
synapse (11.64, 0.000)
microtubuli based transport (5.18, 0.000)
calmodulin binding (4.87, 0.000)
cytoskeleton (3.63, 0.000)
neuropeptide (1.96, 0.012)
signaling from G-protein families (1.49, 0.025)
Renal cell carcinoma (RCC)
RCCpos1 up inflammatory response (12.47, 0.000) NFκB (0.06)1, E2F (0.081)1
regulation of IκB kinase/NFκB (5.54, 0.000) IRF8 (0.000)2, IRF1 (0.000)2, ETS2 (0.000)2, ELF1 (0.000)2, SPI1 (0.000)2, ELF2 (0.001)2, STAT1 (0.001)2, E2F (0.001)2, ETS1 (0.007)2, GABPA (0.007)2, ELK1 (0.010)2, STAT5B (0.021)2, FOXO4 (0.022)2, TP53 (0.024)2, AHR (0.025)2, ETV4 (0.026)2, STAT3 (0.032)2, SMAD1 (0.037)2, IRF7 (0.037)2, AR (0.040)2
angiogenesis (5.17, 0.004)
caspase recruitment (4.8, 0.002)
regulation of transcription (4.03, 0.003)
regulation of apoptosis (3.09, 0.004)
extracellular matrix (2.81, 0.005)
chromatin (2.6, 0.023)
RCCpos2 up semaphorin/CD100 antigen (1.45, 0.023)  
RCCneg1 down mitochondrion (31.99, 0.000) CREB (0.006)1, NRF1 (0.006)1, miR16 (0.068)1
protein catabolic process/proteasome (2.29, 0.037) SF1 (0.000)2, ESRRA (0.000)2, E4F1 (0.006)2, JUN (0.030)2, ATF3 (0.030)2, NRF1 (0.047)2
synaptic vesicle (1.34, 0.029)
  1. Gene ontology (GO) enrichment for the consensus network analysis of the HD caudate nucleus dataset with various diseases. Genes in the identified modules were analyzed using DAVID. The sign of the correlation (cor) 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.