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Table 1 Lists of unique genes contributing to the immune clusters

From: The differential disease regulome

All
clusters
Both NF-κB/Rel
clusters
Both IRF/Stat1/Cutl1
clusters
Both disease
clusters
Both GO
clusters
NF-κB/Rel
cluster (GO)
Gene Hit rate Gene Hit rate Gene Hit rate Gene Hit rate Gene Hit rate Gene Hit rate
HLA-A 22.1% TNF 99.5% TLR4 12.1% HLA-B 30.1% CSF1 19.3% ICAM1 74.7%
NOD2 20.1% LTA 58.3% IL6 9.5% CARD15 22.3% TNFSF13 13.3% IRF6 44.0%
STAT1 12.2% TGFB1 36.9% CTLA4 9.4% VDR 17.5% FLT3LG 8.0% CD69 28.9%
CD40 11.6% CD4 24.8% CCR5 8.5% VEGF 4.1% RELB 6.9% REL 27.7%
TAP1 10.7% AKT1 12.1% TLR3 7.7% NFKBIZ 3.3% CD27 6.0% TNFRSF4 21.1%
NFKBIA 10.7% LTB 11.6% HLA-DRB1 7.2% COL6A1 2.4% PER1 5.9% RELA 18.7%
IRF1 10.1% IL1RN 10.2% IL2 5.9% PSORS1 2.1% PTPN6 5.6% EDC4 16.9%
CXCL10 10.0% IL2RA 10.2% IFNB1 4.2% CYBA 1.7% LCK 5.3% CD58 14.5%
IRF5 7.3% TNFRSF1B 5.3% CCL2 4.1% DDAH2 1.5% MYD88 5.0% TNFRSF18 14.1%
PSMB8 6.7% CD86 5.3% TNFSF13B 3.5% CYP27B1 1.4% PTMA 4.8% CD83 14.1%
PSMB9 6.2% ITGAM 5.1% MX1 3.3% PLAU 1.4% IL27 4.7% TNFRSF9 12.9%
FAS 5.5% TRADD 5.0% STAT5A 3.0% RUNX1 1.3% B2M 4.3% IL17C 12.0%
IL7R 2.6% MIF 3.9% NOD1 3.0% RUNX3 1.2% IRF2 3.1% CD5 10.8%
IFIH1 1.9% NFKBIB 3.4% TLR1 2.9% PAX2 1.1% STAT3 3.0% CD70 9.6%
   CXCL5 3.2% HLA-DMA 2.3% CCND1 1.0% TAPBP 2.9% DPP4 9.6%
   PTGS1 3.0% CASP1 2.1% RXRB 1.0% BIRC3 2.5% NFATC2 9.0%
     SOCS1 1.7% HIF1A 0.8%    TRAF2 9.0%
     TRIM21 1.3%      CREB1 8.0%
     CCL21 1.1%      ...  
  1. Lists of genes that are unique for selected combinations of the four immune-related clusters analyzed (see Figure 4). For each gene, the hit rate (proportion of cluster where the gene is relevant to disease regulation) is presented. The NF-κB/Rel cluster in the Gene Ontology regulome is included because of the large hit rates (only the top of the list is shown). Note that TNF is relevant for regulation for nearly all disease-TF pairs in both NF-κB/Rel-related clusters. The full gene listing is included in Additional file 4.