Table 2 Ingenuity analysis of genes concordantly expressed between DC- and PF-fibroblasts but significantly different in CT

1

ABCG5, Ap1, BIRC3, CASP1, Caspase, CCR6, Creb, CSF2RA (includes EG:1438), DAPP1, DDOST, DMC1, ERK1/2, HNRNPU, IL1, IL18, IL12 (complex), IL17RD, Jnk, LEP, MECOM, NAPB, NFkB (complex), PDGF BB, PNPT1, RAD51, RNF31, SLC12A4, SSTR2, STAT5a/b, SUMO1, TNFSF14, TNFSF15, TP53BP2, UNC5B, XRCC2

47

25

Cell Cycle, DNA Replication, Recombination, and Repair, Metabolic Disease

Pyrimidine Metabolism, Artherosclerosis Signaling, TREM1 Signaling, Glycosphingolipid Biosynthesis-Lactoseries, Death Receptor Signaling, Nucleotide Sugars Metabolism, Aminosugars Metabolism, LXR/RXR Activation, Axonal Guidance Signaling, FXR/RXR Activation, Amyotrophic Lateral Sclerosis Signaling, Endothelin-1 Signaling, N-Glycan Degradation, Cholecystokinin/Gastrin-mediated Signaling, p38 MAPK Signaling, Glycosaminoglycan Degradation, T Helper Cell Differentiation, Graft-versus-Host Disease Signaling, Ovarian Cancer Signaling, Chondroitin Sulfate Biosynthesis, Role of Cytokines in Mediating Communication between Immune Cells, Lymphotoxin β Receptor Signaling, Role of BRCA1 in DNA Damage Response, Dendritic Cell Maturation, Induction of Apoptosis by HIV1, IL-10 Signaling, JAK/STAT Signaling, GM-CSF Signaling, Hypoxia Signaling in the Cardiovascular System, Communication between Innate and Adaptive Immune Cells, Antiproliferative Role of Somatostatin Receptor 2, Linoleic Acid Metabolism, Acute Phase Response Signaling, Acute Myeloid Leukemia Signaling, leptin Signaling in Obesity, Altered T Cell and B Cell Signaling in Rheumatoid Arthritis, Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses, PPAR Signaling, Apoptosis Signaling, IL-6 Signaling, Crosstalk between Dendritic Cells and Natural Killer Cells, p53 Signaling, Chronic Myeloid Leukemia Signaling,

2

ACTR3, ACVR2A, ADCY, AHR, Akt, CAPZA1, CHRNA5, Ck2, CTDP1, ERK, FLNC, FSH, ganglioside GD1b, GATA6, hCG, Histone h3, Histone h4, HSD17B7, Lh, MAGT1, Mapk, MIR124, NELF, NME2, P38 MAPK, PI3K, Pka, PPIB, PROS1, RNA polymerase II, SNAPC4, STAR, STMN1, UPP1, USP49

33

19

DNA Replication, Recombination, and Repair, Drug Metabolism, Endocrine System Development and Function

Pyrimidine Metabolism, Purine Metabolism, N-Glycan Biosynthesis, Axonal Guidance Signaling, Androgen and Estrogen Metabolism, Factors Promoting Cardiogenesis in Vertebrates, Coagulation System, RhoA Signaling, Role of NANOG in Mammalian Embryonic Stem Cell Pluripotency, AMPK Signaling, Estrogen-Dependent Breast Signaling, Activation of IRF by Cytosolic Pattern Recognition Receptors, Wnt/β-catenin Signaling, Caveolar-mediated Endocytosis Signaling, Ephrin Recpetor Signaling, NRF2-mediated Oxidative Stress Response, TGF-β Signaling, Protein Ubiquitination Pathway, Thrombin Signaling, Regulation of Actin-based Motility by Rho, Virus Entry via Endocytic Pathways, Fcy Receptor-mediated Phagocytosis in Macrophages and Monocytes

3

C10ORF58, C6ORF170, CCNB2, CDC7, CPSF4, FBXL12, FCAR, FKBP11, GADD45B, IL9, IL24, Il12 receptor, ITIH3, ITIH5, ITPA, KIAA0101, MAN2B2 (includes EG:23324), MARK3, MCART1, NFYB, PCNA, PFN2, PGRMC1, PILRA, POLD1, PTGS1, RORA, RRAD, STAT4, TBX21, TERT, TGFB1, TGFBR2, XBP1, ZNF394

22

14

Cellular Development, Cell Morphology, Cell-Mediated Immune Response

Pyrimidine Metabolism, Purine Metabolism, Cleavage and Polyadenylation of Pre-mRNA, Eicosanoid Signaling, Endothelin-1 Signaling, N-Glycan Degradation, Arachidonic Acid Metabolism, Ovarian Cancer Signaling,

4

Amino acids, BACE1, BLZF1, C1D, CBR3, CCAR1, CDC6, COL4A3BP, CSNK1G2, EXO1, FEN1, GSTA5, HNF4A, MCM4, MCM5, MCM6, MCM8, MEG3 (includes EG:55384), MLH1, MST1, PMM1, PPARG, PPP1R15B, PRKY, PTGR2, RAB2A, RORC, SAP30BP, SFRS11, SORBS1, STK16, TEAD3, TP53, VDAC2, XPNPEP3

21

14

Tumor Morphology, Cancer, Cell Cycle

Wnt/β-catenin Signaling, Inositol Metabolism,

5

C12ORF24, C3ORF34, C4ORF43, CBR3, CDKN2AIPNL, CEBPB, CYP1A1, D-glucose, DAG1, DCAF13, ETFDH, F7, FKTN, HNF1A, HNF4A, IL1B, INS, LRSAM1, MAPK8, NCK1, NFkB (complex), PHF23, POFUT1, PRR3, SESN2, SLC25A32, SP1, SRC, TSG101, UBE2D3 (includes EG:7323), UBE2N, ZNF557, ZNF577

20

13

Carbohydrate Metabolism, Molecular Transport, Small Molecule Biochemistry

6

ATP, BACE1, C14ORF153, CASP3, CRCP, CTSD, EEF2, EIF2AK3, ERBB2, EREG, ERP29, FUT3, GALNT3, ganglioside GD1a, GHR, GRIPAP1, HIVEP2, HLA-DRA, HRAS, IL24, MSH2, MYO9B, N4BP2, NLRP3, ODZ3, PPP1R15A (includes EG:23645), PRTN3, RFX4, RFXANK, Rsk, SERPINE2, Shc, Sod, SULT1A1, TNF

19

13

Cellular Assembly and Organization, Tissue Morphology, Cell Death

Pyrimidine Metabolism, Purine Metabolism, Cysteine Metabolism, Glycosphingolipid Biosynthesis-Lactoseries, Sulfur Metabolism, Glycosphingolipid Biosynthesis-Neolactoseries, O-Glycan Biosynthesis, Keratan Sulfate Biosynthesis, Chondroitin Sulfate Biosynthesis, BMP Signaling Pathway, NRF2-mediated Oxidative Stress Response, EIF2 Signaling

7

C9ORF80, CDC45L, CTSD, DEFB1, EEF2, Eotaxin, ERAP2, GADD45B, GHR, GRM8, HMGA1, IFNB1, IFNG, IRF9, LILRB3 (includes EG:11025), LIMK1, LMNB2, MSH2, MSH3, MYC, ORC1L, ORC2L, ORC6L, PHC2, PNPT1, RHOB, Rock, ROCK2, RPL7, SEPHS2, SERPING1, STK11, TLE1, TMEM70, UTY

18

12

Cell Cycle, Gene Expression, Inflammatory Response

Pyrimidine Metabolism, Nucleotide Sugars Metabolism, Aminosugars Metabolism, Axonal Guidance Signaling, Cholecystokinin/gastrin-mediated Signaling, Complement System, RhoA Signaling, Glycosaminoglycan Degradation, CCR3 Signaling in Eosinophils, Selenoamino Acid Metabolism, Semaphorin Signaling in Neurons, Acute Phase Response Signaling, Ephrin Receptor Signaling, Chemokine Signaling, Leukocyte Extravasation Signaling, VEGF Signaling, Thrombin Signaling

8

AIRE, C15ORF63, Ca2+, CTSD, D-glucose, DAPK3, EEF2, ganglioside GM3, GBA2, GH1, GHR, GLYCOGEN PHOSPHORYLASE, GPR1, GRB2, heparin, HTT, LTF, MCHR2, MYL2, MYO3B, NISCH, P2RX7, PFN2, PKC ALPHA/BETA, PLA2G12A, PLA2G2D, Pld, PPA2, PPP1R12A, PPP1R1A, PPP3CA, PRF1, SELL, SLC7A9, SORBS1

16

11

Cell Signaling, Molecular Transport, Vitamin and Mineral Metabolism

Primary Immunodeficiency Signaling, Starch and Sucrose Metabolism, Atherosclerosis Signaling, Oxidative Phosphorylation, Eicosanoid Signaling, Cyanoamino Acid Metabolism, Stillbene, Coumanine and Lignin Biosynthesis, Phospholipid Degradation, Endothelin-1 Signaling, p38 MAPK signaling, MIF Regulation of Innate Immunity, CCR3 Signaling in Eosinophils, Arachidonic Acid Metabolism, Glycerophospholipid Metabolism, Linoleic Acid Metabolism

9

ARRB2, beta-estradiol, CCL5, CCL13, CCR5, Creatine Kinase, CSNK1A1L, EEF2, EIF2AK2, FOXO1, GAR1, HSP90AB1, KPNB1, KRI1, LAGE3, NHP2, OSGEP, OTUD5, PCNA, PPM1K, RAF1, RAN, RANGRF, RPLP0 (includes EG:6175), RPS6, SNRPE, SPN, SPRY2, SPRYD5, TACR1, TGFBR2, TNFRSF1B, TRAF3, XPO1, XPO5

16

11

Cell Death, Cell-mediated Immune Response, Cellular Movement

Leukocyte Extravasation Signaling

10

ALPHA AMYLASE, AMY1A, AMY1B, BMP8B, CD44, CSF1, DAG1, DNAH6, DYNLT1, EPO, FOXO1, FOXO3, FYN, glycogen, GRIN1, HCLS1, IL15, INPPL1, KCNH6, LCK, LMOD3, MIR9-1 (includes EG:407046), NMT1, oleic acid, PLCG2, Pld, PLIN5, RPS4Y2, Shc, SHC1, SHCBP1, TDRD1, VCAM1, VEGF

15

11

Cellular Development, Cell Cycle, Cell Death

Starch and Sucrose Metabolism, Factor Promoting Cardiogenesis in Vertebrates, Role of NANOG in Mammalian Embryonic Stem Cell Pluripotency, Role of Osteoblasts, Osteoclasts and Chondrocytes in Rheumatoid Arthritis, Basal Cell Carcinoma Signaling, BMP Signaling

11

ASB1, BEGAIN, C1ORF9, C8ORF45, CCDC85B, CTSD, DEFB103A, Eotaxin, EREG, ganglioside GD1a, ganglioside GD1b, ganglioside GM1, ganglioside GM2, ganglioside GM3, ganglioside GT1, GHR, IL32, KIAA0408, LHX4, MAFF, MAPK1, MIR202 (includes EG:387198), NDUFA5, NEUROG3, NRP1, PCBP2, PDE4C, PSAP, ROBO1, SEMA3D, SEMA3E, Sphk, TNF, ZFP36, ZNF337

14

12

Lipid Metabolism, Small Molecule Biochemistry, Cell Morphology

Purine Metabolism, Aminosugars Metabolism, Oxidative Phosphorylation, Lipid Antigen Presentation by CD1, Axonal Guidance Signaling, Ubiquinone Biosynthesis

12

ACTN1, BCAS2, C16ORF72, COPS2, CTTNBP2, CTTNBP2NL, DNTTIP2, EGR1, ESR1, ESR2, FAM40A, FAM40B, FAM63B, G alphai, JUN, MCC, MCM2, MIR122, MIR214 (includes EG:406996), MOBKL3, NR0B1, NR2F1, NRIP1, PPP2R1A, PTEN, retinoic acid, RNF122, RP6-213H19.1, SIKE1, STK24, STK25, STRN, STRN3, TRAF3IP3

9

7

Gene Expression, Cellular Development, Cellular Growth and Proliferation

Oxidative Phosphorylation