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. 2016 Jul 2;8:836–850. doi: 10.1016/j.dib.2016.06.051

Table 2.

Gene sets significantly modulated by Aminaphtone in treated vs. untreated IL-1β-stimulated endothelial cells.

GO Categorya GO Ontology GO term #genes LS KS Gene list
0005975 BP carbohydrate metabolic process 11 0.0805 0.0028 DDIT4, ENO2, FUT11, GCLC, HK2, HMMR, PDGFB, PDK1, PFKFB4, PPP1R3C, SLC2A1
0007166 BP cell surface receptor signaling pathway 46 0.0260 0.0020 AAK1, BCL2L11, BMP6, CBLB, CITED2, CX3CL1, DDIT4, DDR1, DKK1, EBI3, ECT2, EDN1, EFNA1, EFNB2, EIF4B, EIF4EBP2, FOS, FST, GAREM, GPR56, GRB7, IL1B, IL7R, KCTD11, LIF, MERTK, OXTR, PDGFB, PIK3R1, PIK3R3, PLAT, PLEKHG2, PRDM1, PRKCA, PTCH1, SEMA4C, STAT5A, STC1, STC2, TGFB1I1, TGFB2, TICAM1, TLE1, TNFSF18, ULK1, VLDLR
0022411 BP cellular component disassembly 7 0.0042 0.8859 BNIP3, DDIT4, DDR1, MMP1, MMP10, MMP3, TOP2A
0048732 BP gland development 11 0.0031 0.0022 BCL2L11, CITED2, DDR1, ELF3, HK2, ID2, OXTR, PDGFB, PTCH1, STAT5A, TGFB2
0042592 BP homeostatic process 26 0.0015 0.2886 BCL2L11, BNIP3, CITED2, CTSK, EDN1, EGR2, GCLC, GCLM, GPR89A, HK2, HMOX1, ID2, IL1B, IL7R, MYLIP, OXTR, POLA1, PRKCA, PTCH1, SERPINA3, STAT5A, STC1, STC2, TFRC, TGFB2, TNFRSF11B
0002376 BP immune system process 47 0.0015 0.0284 ANXA3, BCL2L11, BCL3, BMP6, BNIP3, CBLB, CCL22, CD70, CD83, CITED2, CLEC4E, CSF2, CTSK, CX3CL1, CXCL3, CXCL6, DDIT4, EBI3, EDN1, FOS, FST, GRB7, HMOX1, ID2, IL1B, IL32, IL7R, KIF23, LIF, MARCH8, MERTK, MMP1, PDGFB, PIK3R1, PIK3R3, PODXL, PRDM1, PRKCA, SELE, SERPINB9, STAT5A, TFRC, TGFB2, TICAM1, TNFSF18, ULBP3, ZC3HAV1
0006954 BP inflammatory response 15 0.0131 0.0047 BMP6, CCL22, CX3CL1, CXCL3, CXCL6, ELF3, FOS, HMOX1, IL1B, PRKCA, SELE, SERPINA3, STAT5A, TICAM1, TNFAIP6
0043066 BP negative regulation of apoptotic process 20 0.0028 0.0677 AGAP2, BCL3, BNIP3, CITED2, CSF2, CTH, CX3CL1, EDN1, GCLC, GCLM, HMOX1, IL1B, NR4A2, NUAK2, PIK3R1, PRKCA, SERPINB9, STAT5A, TLE1, TNFSF18
0007389 BP pattern specification process 6 0.0137 0.0006 CITED2, DKK1, EDN1, EGR2, FST, PTCH1
0010646 BP regulation of cell communication 49 0.1744 0.0034 AAK1, ACAP1, AGAP2, ANKRD1, ARHGEF26, BCL2L11, BCL3, BMP6, BNIP3, CBLB, CITED2, CSF2, CTH, DDIT4, DKK1, DUSP8, ECT2, EDN1, EFNA1, EGR2, FST, GAREM, GPR89A, HMOX1, IL1B, KCTD11, LIF, LMCD1, OXTR, PDGFB, PHLDA3, PLAT, PLEKHG2, PRDM1, PRKCA, PTCH1, RASD2, SEMA4C, SLC2A1, SPRY4, SYDE1, TGFB1I1, TGFB2, TICAM1, TLE1, TRAF1, TRIP6, ULK1, ZC3HAV1
0042127 BP regulation of cell proliferation 23 0.0019 0.0322 BMP6, BRCA1, CBLB, CSF2, DDR1, EBI3, EDN1, GAREM, HILPDA, HMOX1, ID2, IL1B, KCTD11, LIF, PDGFB, PRDM1, PRKCA, PTCH1, STAT5A, TGFB1I1, TGFB2, TICAM1, TNFSF18
0045619 BP regulation of lymphocyte differentiation 5 0.0009 0.0034 CD83, ID2, IL7R, PRDM1, STAT5A
0051246 BP regulation of protein metabolic process 38 0.0567 0.0032 AGAP2, BCL3, BMP6, BRCA1, BUB1B, CBLB, CSF2, DDIT4, DKK1, DUSP8, EBI3, ECT2, EDN1, EFNA1, EIF4B, EIF4EBP2, GCLC, GRB7, HMOX1, IL1B, KRT17, LIF, LPIN1, MYLIP, PDGFB, PLAT, PRKCA, RASD2, SAMD4A, SERPINA3, SERPINB9, SERPINH1, SERPINI1, SPRY4, STAT5A, TGFB2, TICAM1, VLDLR
0051090 BP regulation of sequence-specific DNA binding transcription factor activity 10 0.0020 0.0058 ANXA3, CTH, FOS, HMOX1, ID2, IL1B, PTCH1, TICAM1, TNFSF18, TRAF1
0006357 BP regulation of transcription from RNA polymerase II promoter 30 0.0035 0.6000 ANKRD1, BCL3, BMP6, BRCA1, CITED2, DKK1, EDN1, EFNA1, EGR2, ELF3, ERF, FOS, FST, HMOX1, ID2, IL1B, LIF, LMCD1, LPIN1, MEF2D, NR4A2, PER1, PIK3R1, POLA1, PRDM1, PTCH1, RRM2, STAT5A, TOP2A, VLDLR
0036293 BP response to decreased oxygen levels 14 0.0024 0.0002 ANKRD1, BNIP3, CITED2, DDIT4, EDN1, HMOX1, NR4A2, OXTR, PDGFB, PDK1, PLAT, STC1, STC2, TGFB2
0009605 BP response to external stimulus 32 0.0001 0.0071 AGAP2, ANKRD1, BNIP3, CCL22, CITED2, CX3CL1, CXCL3, CXCL6, CYP24A1, EDN1, EFNB2, EGR2, ELOVL4, FOS, HMOX1, ID2, IL1B, NR4A2, NUAK2, PDGFB, PER1, PLAT, PRKCA, RND1, SELE, SLC2A1, STAT5A, STC1, STC2, TGFB2, TNFRSF11B, ULK1
0010033 BP response to organic substance 48 <0.0001 0.0168 ANKRD1, BMP6, BRCA1, CD83, CITED2, CSF2, CTH, CX3CL1, CYP24A1, DKK1, DNAJB1, EBI3, EDN1, EGR2, EIF4B, EIF4EBP2, FOS, GAREM, GCLC, HCAR1, HMOX1, IDI1, IL1B, IL7R, LOX, LPIN1, MMP3, NR4A2, OXTR, PDGFB, PIK3R1, PIK3R3, PLAT, PRDM1, PRKCA, PTCH1, SELE, SERPINB9, SERPINH1, STAT5A, STC1, STC2, TGFB1I1, TGFB2, TICAM1, TNFRSF11B, TNFSF18, ZC3HAV1
0048511 BP rhythmic process 6 0.0033 0.0194 EGR2, ID2, OXTR, PER1, STAT5A, TGFB2
0046903 BP secretion 20 0.0238 0.0008 ANKRD1, ANXA3, BMP6, CLEC4E, DDR1, EDN1, FST, HK2, HMOX1, IL1B, LIF, MERTK, OXTR, PDGFB, PRKCA, SLC2A1, SRGN, STAT5A, TGFB2, VAMP1
0005125 MF cytokine activity 15 0.0061 0.0047 BMP6, CCL22, CD70, CSF2, CX3CL1, CXCL3, CXCL6, EBI3, EDN1, IL1B, IL32, LIF, TGFB2, TNFRSF11B, TNFSF18
0004175 MF endopeptidase activity 6 0.0004 0.1037 CTSK, MMP1, MMP10, MMP3, PLAT, PRSS22
0001071 MF nucleic acid binding transcription factor activity 11 0.0006 0.0382 BCL3, CEBPD, CITED2, EGR2, ELF3, ERF, FOS, MEF2D, NR4A2, PRDM1, STAT5A
0000988 MF protein binding transcription factor activity 11 0.0990 0.0032 ANKRD1, BRCA1, CITED2, ELF3, ERF, LIF, LMCD1, LPIN1, PER1, TGFB1I1, TLE1
0019904 MF protein domain specific binding 5 0.0031 0.0167 ACAP1, CITED2, EGR2, IL1B, KHDRBS3
0001067 MF regulatory region nucleic acid binding 6 0.0040 0.0378 BRCA1, EGR2, FOS, MEF2D, PER1, STAT5A
0031012 CC extracellular matrix 9 0.0034 0.0040 LAMB3, LMCD1, LOX, MMP1, MMP10, MMP3, TGFB1I1, TGFB2, TNFRSF11B
0005615 CC extracellular space 31 0.0003 <0.0001 BMP6, CCL22, CD70, CSF2, CTSK, CX3CL1, CXCL3, CXCL6, DKK1, EBI3, EDN1, HILPDA, HMOX1, IGFL1, IL1B, IL32, LIF, LMCD1, LOX, MERTK, MMP10, MMP3, PLAT, SELE, SERPINB9, SRGN, STC1, TGFB2, TNFRSF11B, TNFSF18, VLDLR



KEGG Pathwayb Pathway description #genes LS KS Gene list
hsa04060 Cytokine-cytokine receptor interaction 13 0.0287 0.0095 CCL22, CD70, CSF2, CX3CL1, CXCL3, CXCL6, IL1B, IL7R, LIF, PDGFB, TGFB2, TNFRSF11B, TNFSF18



Broad MSigDB Curated Gene Setc #genes LS KS Gene list
HINATA_NFKB_TARGETS_KERATINOCYTE_UP 13 0.0004 0.0095 CD83, CSF2, CXCL3, CXCL6, EFNA1, IL1B, IL32, IL7R, MMP1, PLAT, STAT5A, TNFAIP6, TRAF1
HINATA_NFKB_TARGETS_FIBROBLAST_UP 6 0.0027 0.1123 CD83, CXCL3, CXCL6, IL1B, MMP1, SELE
SCHOEN_NFKB_SIGNALING 5 0.0192 0.0036 CSF2, EDN1, IL1B, NUAK2, SERPINA3
ELVIDGE_HYPOXIA_UP 19 0.0017 0.0010 AK4, BNIP3, CITED2, DDIT4, DDR1, ELF3, ENO2, FOS, HK2, LOX, P4HA1, PDGFB, PDK1, PRKCA, SAMD4A, SLC2A1, STC1, STC2, VLDLR
ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN 14 0.0036 0.0001 AK4, BNIP3, CITED2, ENO2, FOS, HK2, LOX, P4HA1, PDGFB, PDK1, SAMD4A, SLC2A1, STC1, VLDLR
ELVIDGE_HYPOXIA_BY_DMOG_UP 17 0.0038 0.0023 AK4, BNIP3, CITED2, DDIT4, ELF3, ENO2, FOS, HK2, LOX, P4HA1, PDK1, PRKCA, SAMD4A, SLC2A1, STC1, STC2, VLDLR
ELVIDGE_HIF1A_TARGETS_DN 13 0.0114 0.0002 AK4, BNIP3, CITED2, ENO2, FOS, HK2, LOX, P4HA1, PDGFB, PDK1, SLC2A1, STC1, VLDLR
WINTER_HYPOXIA_METAGENE 18 0.0022 0.0376 BNIP3, CITED2, DDIT4, EDN1, EFNA1, ELF3, FOS, HK2, HMOX1, ID2, LOX, P4HA1, PDGFB, PFKFB4, SLC2A1, SLC6A8, STC2, TFRC
PID_HIF1_TFPATHWAY 9 0.0022 0.2078 BNIP3, CITED2, EDN1, FOS, HK2, HMOX1, ID2, SLC2A1, TFRC
MENSE_HYPOXIA_UP 10 0.0028 0.0004 BNIP3, CEBPD, ENO2, HK2, LOX, P4HA1, PDK1, PFKFB4, PPP1R3C, STC2
LEONARD_HYPOXIA 11 0.0061 0.0007 AK4, BNIP3, DDIT4, EFNA1, HK2, P4HA1, PDGFB, PFKFB4, PPP1R3C, SLC2A1, STC2
JIANG_HYPOXIA_NORMAL 15 0.0134 0.0009 AK4, BNIP3, CITED2, CNNM4, EIF4B, ENO2, HMOX1, KHDRBS3, LOX, P4HA1, PFKFB4, PPP1R3C, RIPK4, SLC2A1, STC2
KRIEG_HYPOXIA_VIA_KDM3A 5 0.0182 0.0026 C15orf48, CLEC4E, EDN1, HMOX1, LAMB3
FARDIN_HYPOXIA_11 6 0.0200 0.0029 AK4, BNIP3, DDIT4, FUT11, PDK1, PFKFB4
NAGASHIMA_EGF_SIGNALING_UP 8 0.0008 0.0007 AREG, DNAJB1, EDN1, EGR2, FOS, LIF, NR4A2, TNFRSF11B
ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP 22 0.0021 0.0070 BCL3, C15orf48, CD83, CXCL3, DDIT4, EDN1, EFNA1, GCLC, IGFL1, IL1B, IL32, IL7R, LAMB3, LIF, MMP10, NAV3, NINJ1, SAMD4A, SEMA4C, SERPINB9, TNFAIP6, TRAF1
BASSO_CD40_SIGNALING_UP 8 0.00498 0.0093 CCL22, CD83, DDIT4, IL1B, PTP4A3, SRGN, STAT5A, TRAF1
WIERENGA_STAT5A_TARGETS_GROUP2 5 0.0163 0.0036 CCL22, CD83, CSF2, IL7R, TRAF1

GO ontology: BP=biological process, MF=molecular function, and CC=cellular component.

a

GO (Gene Ontology) categories,

b

KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, and

c

MsigDB (Broad Institute Molecular Signature Database) curated gene sets found to be significant at the 0.005 significance level of either the LS or KS permutation tests. For each Gene Set, the table lists the unique identifier, the number of genes differentially modulated, the Fisher (LS) and Kolmogorov–Smirnov (KS) permutation P-values (P-values <0.005 are in bold), and the list of modulated genes.