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Table 2 Functional classification of NF-κB-dependent genes.

From: A TNF-induced gene expression program under oscillatory NF-κB control

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

  1. 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.
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BMC Genomics

ISSN: 1471-2164

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