Table 2.
Functional classification of NF-κB-dependent genes.
| Function | Name | GenBank | Locus | Pr(F) | Cluster | Function | Name | GenBank | Locus | Pr(F) | Cluster |
| Anti-apoptosis | Receptors | TAP1 | X57522 | 6p21.3 | 1E-08 | Late | |||||
| BID | AF042083 | 22q11.1 | 1E-07 | Middle | TAPBP | AF029750 | 6p21.3 | 1.2E-07 | Late | ||
| BIRC2 | U37547 | 11q22 | 0.00017 | Middle | NK4 | AA631972 | 16p13.3 | 4E-08 | Late | ||
| TNFAIP3 | M59465 | 6q23 | 4.67E-11 | Early | KCNG1 | AL050404 | 20q13 | 1.21E-10 | Paradox | ||
| Cytokine | ITGB5 | X53002 | 3q21.2 | 0.003318 | Paradox | ||||||
| IL8 | M28130 | 4q13 | 4.02E-08 | Early | GPR49 | AF062006 | 12q22 | 0.006668 | Paradox | ||
| IL6 | X04430 | 7p21 | 8.89E-08 | Early | CHRNB4 | U48861 | 15q24 | 0.00637 | Paradox | ||
| TNF | X02910 | 6p21.3 | 0.002926 | Early | F2RL1 | U67058 | 5q13 | 2.67E-05 | Paradox | ||
| CXCL1/Gro-a | X54489 | 4q21 | 6.04E-07 | Early | AQP3 | N74607 | 9p13 | 0.008818 | Biphasic | ||
| CXCL3/Gro-g | M36821 | 4q21 | 4.62E-08 | Early | Signaling | ||||||
| CXCL2/Gro-b | M36820 | 4q21 | 9.88E-15 | Early | IkBe | U91616 | 6p21.1 | 1.10E-10 | Middle | ||
| CCL20/Exodus-1 | U64197 | 2q33 | 1.96E-07 | Early | BCL3 | U05681 | 19q13.1 | 8.44E-05 | Middle | ||
| Growth Factors/Secreted Proteins | TRAF2 | U12597 | 9q34 | 0.001067 | Middle | ||||||
| TNFAIP2/B94 | M92357 | 14q32 | 1.20E-09 | Middle | TRAF1 | U19261 | 9q33-q34 | 5.87E-07 | Late | ||
| Comp B | L15702 | 6p21.3 | 1.2E-08 | Middle | TRAF3 | U21092 | 14q32.33 | 0.000139 | Late | ||
| EFNA1 | M57730 | 1q21 | 8.34E-05 | Early | IkBa | M69043 | 14q13 | 5.55E-15 | Early | ||
| Follistatin | M19481 | 5q11.2 | 2.26E-05 | Paradox | PTGS2 | U04636 | 1q25.2 | 3.43E-08 | Early | ||
| CTGF | X78947 | 6q23.1 | 3.6E-06 | Paradox | PPP1R3C | N36638 | 10q23-q24 | 0.000734 | Paradox | ||
| SCGF | AF020044 | 19q13.3 | 0.002939 | Paradox | DUSP4 | U48807 | 8p12 | 8.4E-06 | Paradox | ||
| Metabolic | PTGES | AF010316 | 9q34.3 | 0.002286 | Late | ||||||
| SOD2 | X07834 | 6q25.3 | 2.98E-07 | Middle | Transcription factor | ||||||
| GCH1 | U19523 | 14q22.1 | 3.93E-07 | Middle | NF-kB1 | M58603 | 4q24 | 1.73E-08 | Middle | ||
| GFPT2 | AB016789 | 5q34-q35 | 8.00E-10 | Middle | RELB | M83221 | 19q13.32 | 4.00E-14 | Middle | ||
| TIMP2 | U44385 | 17q25 | 0.009703 | Paradox | NFKB2 | X61498 | 10q24 | 3.62E-14 | Late | ||
| HES1 | L19314 | 3q28 | 0.000133 | Paradox | REL | X75042 | 2p13 | 0.00011 | Early | ||
| CYB5 | L39945 | 18q23 | 0.005638 | Biphasic | IRF1 | L05072 | 5q31.1 | 1.79E-06 | Early | ||
| PSMB9 | AA808961 | 6p21.3 | 1E-09 | Biphasic | TRIM16 | AF096870 | 17p11.2 | 0.000221 | Late | ||
| PSMB8 | X87344 | 6p21.3 | 0.007828 | Biphasic | Unknown | ||||||
| Receptor/cell surface | Unknown | HG371-HT26388 | - | 7.53E-05 | Late | ||||||
| KLRC3 | AJ001685 | 12p13 | 0.000029 | Middle | TNIP1/Naf-1 | AJ011896 | 5q32 | 1.00E-11 | Late | ||
| SDC4 | D79206 | 20q12 | 6.60E-08 | Middle | PLAU | X02419 | 10q24 | 0.000399 | Early | ||
| SLC7A2 | D29990 | 8p22 | 0.004933 | Middle | OLFML2A | AL050002 | 9q34.11 | 0.000027 | Paradox | ||
| CD83 | Z11697 | 6p23 | 1.50E-11 | Middle | 31 | HBE1 | AI349593 | 11p15.5 | 2E-07 | Paradox | |
| IFNGR2 | U05875 | 21q22.11 | 4.18E-06 | Middle | chimeric | Y15915 | - | 0.005238 | Paradox | ||
| ECE1 | Z35307 | 1p36.1 | 0.004074 | Middle | DLX2 | U51003 | 2q32 | 0.008043 | Paradox | ||
| KLRC2 | AJ001684 | 12p13 | 0.000822 | Late | Transgelin | D17409 | 11q23.2 | 0.00012 | Paradox | ||
| ICAM1 | M24283 | 19p13.3 | 0.000124 | Late | IFI35 | U72882 | 17q21 | 0.004532 | Biphasic | ||
| IL27RA | AI263885 | 19p13.11 | 6E-09 | Late | MVP | X79882 | 16p13.1 | 0.004212 | Biphasic | ||
The 74 NF-κB dependent probe sets were analyzed. Duplicate probe sets (e.g., those mapping to the same gene) were eliminated and unique genes tabulated. For each gene identified, the primary cellular function (Function), the common name (Name), the Genbank Accession number (GenBank), the chromosomal locus (Locus), the p-value indicating its significance that its expression is affected by NF-κB [Pr(F)], and its Cluster location (Cluster). Clusters are colored according to indicated expression pattern. Abbreviations used are: BID, BH3 domain interacting agonist; BIRC3, IAP homolog 3; TNFAIP3, TNF alpha induced protein3 (A20); IL, interleukin; CXCL, CXC motif ligand; CCL, CC motif ligand; Comp B, complement factor B; EFNA1, ephrin-A1: CTGF, connective tissue growth factor; SCGF, stem cell growth factor; SOD, superoxide dismutase; GCH1; GTP cyclohydrolase; GFPT2, glutamine-fructose-6-phosphate transaminase 2; PSMB, proteasome subunit; CYB5, cytochrome B5, HES, hairy enhancer of split; TIMP, tissue inhibitor of metalloprotein;, KLRC, SDC4, syndecan 4; SCLC7A2, human cationic transporter; IFNGR2, IFN gamma receptor 2; ECE, endothelial converting enzyme; KLRC2, natural lectin killer receptor 2; ICAM, intercellular adhesion molecule; IL27RA, interleukin 27 receptor alpha; TAP, transporter of antigen peptide; TAPBP, TAP binding protein; NK4, natural killer receptor 4; AQP3, aquaporin 3; KCNG1, potassium voltage-gated channel; ITGB5, integrin beta 5; GPR49, orphan G coupled receptor 49; CHRNB4 beta 4 nicotinic acetylcholine receptor; F2RL1, proteinase activated receptor -2; BCL-3, B cell lymphoma 3; TRAF, TNF receptor associated factor; PTGES, prostaglandin endoperoxide synthase; PTGS2, prostaglandin synthase 2; PPP1R3C, regulatory subunit of protein phosphatase 1; DUSP, dual specificity phosphatase; IRF, interferon response factor; TRIM 16, tripartite motif containing-16/estrogen responsive B-Box protein; TNIP/Naf-1, TNF inducible protein/Nef-associated factor-1; MVP, major vault protein; PLAU, urokinase plasminogen-activator gene; OLFML2A, olfactomedin-like 2A; HBE1, hemoglobin epsilon chain; DLX2, distal-less homeobox2.