Table 1

All genes upregulated or downregulated by ibuprofen in the presence of IL-1β with FC ≥1.5 in either direction

GeneNameFunctionMean (IL1)Mean (IL1 +ibu)FCadj. P
PPARGPeroxisome proliferator activated receptor gammaCarbohydrate and lipid metabolism, inflammation0.30.92.875.0E−06
UMODL1Uromodulin like 1Regulation of apoptosis?0.30.72.390.0011
XIRP1Xin actin binding repeat containing 1Actin binding5.713.42.38< 1.0E−06
DACT1Dishevelled binding antagonist of beta catenin 1Regulation of cell cycle and tissue development48.42.1< 1.0E−06
CSF2/GM-CSFColony stimulating factor 2=Granulocyte-macrophage colony stimulating factorLeucocyte differentiation, immune response5.211.22.09< 1.0E−06
PPARGC1BPPARG coactivator 1 betaRegulation of transcription0.40.82.070.00024
FAM186BFamily with sequence similarity 186 member B?0.40.71.920.0035
SOX17SRY-box 17Cell proliferation, tissue development3.56.81.91< 1.0E−06
MTSS1MTSS1, I-BAR domain containingCell adhesion6.912.61.9< 1.0E−06
AKAP6A-kinase anchoring protein 6Regulation of cell proliferation, cAMP signalling2.13.91.89< 1.0E−06
PDE5APhosphodiesterase 5ARegulation of NO signalling1.22.31.857.0E−06
RGS2Regulator of G protein signalling 2Regulation of G protein signalling52.195.91.85< 1.0E−06
CAMK2ACalcium/calmodulin dependent protein kinase II alphaWnt and TGFβ signalling, NF-κB activation1.83.31.81< 1.0E−06
MAP1LC3CMicrotubule associated protein 1 light chain 3 gammaAutophagy0.71.21.793.3E−05
NRG1Neuregulin 1Cell differentiation, signal transduction0.71.31.785.9E−05
SELESelectin EInflammation41.373.51.78< 1.0E−06
FCRLAFc receptor like AImmunoglobulin binding4.27.41.76< 1.0E−06
DENND3DENN domain containing 3Autophagy14.625.31.75< 1.0E−06
FCRLBFc receptor like BImmunoglobulin binding0.81.41.733.3E−05
MOXD1Monooxygenase DBH like 1Monoamine metabolism123.1210.31.72< 1.0E−06
SPNS2Sphingolipid transporter 2Lipid transport2.44.01.72< 1.0E−06
PODXLPodocalyxin likeCell adhesion11.219.01.71< 1.0E−06
RP1RP1, axonemal microtubule associated?0.40.61.670.023
IDO1Indoleamine 2,3-dioxygenase 1Modulation of inflammation and cartilage development1.32.11.650.0012
SCUBE3Signal peptide, CUB domain and EGF like domain containing 3TGFβ signalling42.572.51.64< 1.0E−06
KCNJ15Potassium voltage-gated channel subfamily J member 15Potassium transport1.32.21.631.0E−06
SERPINE1Serpin family E member 1Inhibition of proteolysis455.9748.61.62< 1.0E−06
PSD2Pleckstrin and Sec7 domain containing 2?0.40.61.620.035
LINGO1Leucine rich repeat and Ig domain containing 1?1.93.11.61< 1.0E−06
AKNAD1AKNA domain containing 1?0.61.01.600.0048
STRA6Stimulated by retinoic acid 6Retinol and adipokine binding1.92.91.590.00058
ITGAXIntegrin subunit alpha XCell adhesion11.017.41.58< 1.0E−06
KCNN3Potassium calcium-activated channel subfamily N member 3Potassium transport2.84.31.58< 1.0E−06
ICAM5Intercellular adhesion molecule 5Cell adhesion4.57.21.58< 1.0E−06
FGD4FYVE, RhoGEF and PH domain containing 4Cytoskeleton organisation21.934.01.57< 1.0E−06
KCNN4Potassium calcium-activated channel subfamily N member 4Potassium transport6.410.01.57< 1.0E−06
LRRC55Leucine rich repeat containing 55Potassium transport0.81.31.560.0013
CXCR3C-X-C motif chemokine receptor 3Inflammation0.71.11.550.017
CD24CD24 moleculeWnt and MAPK signalling, regulation of inflammation5.48.51.55< 1.0E−06
FGRFGR proto-oncogene, Src family tyrosine kinasePI3K-Akt signalling, regulation of inflammation3.45.21.54< 1.0E−06
PEG10Paternally expressed 10Inhibition of TGFβ signalling23.936.41.54< 1.0E−06
SIGLEC15Sialic acid binding Ig like lectin 15Regulation of bone resorbtion1.62.41.540.00024
CPNE2Copine 2Bone erosion18.728.91.54< 1.0E−06
WNK4WNK lysine deficient protein kinase 4Ion transport4.67.01.53< 1.0E−06
RTL3Retrotransposon Gag like 3Regulation of collagen production3.35.01.53< 1.0E−06
RGS3Regulator of G protein signalling 3Inhibition of MAPK signalling65.199.21.52< 1.0E−06
AOC2Amine oxidase, copper containing 2Amine metabolism68.0102.31.51< 1.0E−06
IL10RAInterleukin 10 receptor subunit alphaRegulation of inflammation1.01.61.510.0018
RGS16Regulator of G protein signalling 16?60.190.01.51< 1.0E−06
PCDH17Protocadherin 17Cell adhesion0.91.41.510.028
GPR158G protein-coupled receptor 158?1.31.91.500.00017
IL23AInterleukin 23 subunit alphaInflammation15.24.73.24< 1.0E−06
HAS1Hyaluronan synthase 1Extracellular matrix production0.80.32.77< 1.0E−06
IGFBP4Insulin-like growth factor binding protein 4Cell proliferation and metabolism213.879.72.73< 1.0E−06
IL6Interleukin 6Inflammation958.4403.82.49< 1.0E−06
PDE3APhosphodiesterase 3ALipid metabolism0.90.32.480.00013
STAT4Signal transducer and activator of transcription 4Inflammation, regulation of cell proliferation2.51.02.36< 1.0E−06
PCSK1Proprotein convertase subtilisin/kexin type 1Metabolism7.23.22.19< 1.0E−06
ADAMTS6ADAM metallopeptidase with thrombospondin type 1 motif 6Extracellular matrix catabolism10.54.92.18< 1.0E−06
HALHistidine ammonia-lyaseHistidine catabolism1.70.82.12< 1.0E−06
DNAH17Dynein axonemal heavy chain 17Cytoskeleton component1.00.52.062.00E−06
CSF3Colony stimulating factor 3Inflammation, regulation of cell proliferation19.89.92.02< 1.0E−06
AREGAmphiregulinEGF signalling, regulation of cell proliferation2.31.22.01< 1.0E−06
CA12Carbonic anhydrase 12Acidity regulation, Regulation of proliferation20.910.52.00< 1.0E−06
INSCInscuteable homolog (Drosophila)Cell differentiation0.60.31.980.0011
KCNE5Potassium voltage-gated channel subfamily E regulatory subunit 5Regulation of potassium transport1.30.61.946.00E−06
LDB2LIM domain binding 2Regulation of transcription0.50.31.920.005098
DOK6Docking protein 6?0.90.51.800.000598
DAW1Dynein assembly factor with WD repeats 1Dynein assembly0.90.51.780.000565
TMEM71Transmembrane protein 71?1.81.01.772.00E−06
MAMSTRMEF2 activating motif and SAP domain containing transcriptional regulatorRegulation of transcription0.50.31.720.021819
KNDC1Kinase non-catalytic C-lobe domain containing 1?0.80.51.700.002773
EFHC2EF-hand domain containing 2Cell proliferation0.80.51.690.004747
MEX3AMex-3 RNA binding family member API3K-Akt signalling0.90.51.690.001905
TGFBITransforming growth factor beta inducedECM organisation, chondrocyte differentiation127.880.71.64< 1.0E−06
C3AR1Complement C3a receptor 1Inflammation3.52.21.63< 1.0E−06
EFEMP1EGF containing fibulin like extracellular matrix protein 1Inhibition of chondrocyte differentiation72.645.41.63< 1.0E−06
NAMPTNicotinamide phosphoribosyltransferase / visfatinCartilage catabolism596.1368.81.60< 1.0E−06
FOXF1Forkhead box F1Morphogenesis1.20.81.600.000928
AVPI1Arginine vasopressin induced 1MAPK signalling39.724.81.60< 1.0E−06
SEMA3ASemaphorin 3ARegulation of inflammation and apoptosis98.061.61.59< 1.0E−06
STC1Stanniocalcin 1Regulation of cartilage development2.01.31.590.002967
TSKUTsukushi, small leucine rich proteoglycan?14.99.41.58< 1.0E−06
SMOC1SPARC related modular calcium binding 1ECM organisation199.0126.11.57< 1.0E−06
ARAP2ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2Cell adhesion, inhibition of Akt signalling12.58.01.56< 1.0E−06
BEND5BEN domain containing 5Negative regulation of transcription0.90.61.540.01673
EPB41L3Erythrocyte membrane protein band 4.1 like 3Cortical cytoskeleton organisation34.622.51.53< 1.0E−06
EPB41L4BErythrocyte membrane protein band 4.1 like 4BRegulation of cell adhesion and gene expression2.81.81.530.000106
ACSL4Acyl-CoA synthetase long-chain family member 4Lipid metabolism428.1280.71.52< 1.0E−06
NR4A2Nuclear receptor subfamily 4 group A member 2Wnt signalling, regulation of apoptosis19.813.11.51< 1.0E−06
PID1Phosphotyrosine interaction domain containing 1Oxidative metabolism285.1190.61.51< 1.0E−06
RSPO3R-spondin 3Wnt signalling, morphogenesis82.953.81.50< 1.0E−06
  • Red = upregulated genes; blue = downregulated genes.

  • adj. P, False discovery rate (FDR) -adjusted P value; IL, interleukin; Mean, trimmed mean of M-values (TMM) normalized counts.