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Table 2 Putative transcription factor binding sites of clusters A and B over-expressed in HNSCC

From: Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma

Gene name

Gene description

RefSeq

Orthloga

Number of TFBSs predictedb

Functional annotationc

    

p53

NF-κB

AP-1

STAT3

EGR1

 

Cluster A

ABCC5

ATP-binding cassette, subfamily C (CFTR/MRP), member 5

NM_005688

hmra

   

1 (hmr)

 

Transport

ARID1A

AT rich interactive domain 1a (SWI-like)

NM_006015

hmr

1 (hmr)

   

5 (hmr)

Regulation of metabolism

ARTS-1

Type 1 TNF receptor shedding aminopeptidase regulator

NM_016442

hmr

1

1

 

1

1

Catabolism

ATP1B3

ATPase, Na+/K+ transporting, beta 3 polypeptide

NM_001679

hmr

 

3

  

7

Transport

BLK

B lymphoid tyrosine kinase

NM_001715

hmr

  

1

  

Signal transduction

CDC42EP4

cdc42 effector protein 4; binder of Rho GTPases 4

NM_012121

h

1

2

 

2

 

Regulation of cell shape

CDH18

Cadherin 18, type 2

NM_004934

h

     

Cell adhesion

CDKN2C

Cyclin-dependent kinase inhibitor 2C (p18)

NM_078626

hmr

3

1

   

Cell proliferation; cell cycle

CKB

Creatine kinase, brain

NM_001823

hmr

 

3

  

8

Creatine kinase activity

CPS1

Carbamoyl-phosphate synthetase 1, mitochondrial

NM_001875

hmr

2 (hmr)

1

1 (hmr)

  

Amino acid metabolism

FZD1

Frizzled homolog 1 (Drosophila)

NM_003505

h

 

1

  

4

Signal transduction

HARSL

Histidyl-tRNA synthetase-like

NM_012208

hm

 

2

 

1

1

Amino acid metabolism

HBE1

Hemoglobin, epsilon 1

NM_005330

hr

 

1

 

1

 

Transport

HIST1H2AC

H2A histone family, member L

NM_003512

h

 

1

   

Chromosome organization and biogenesis

HIST1H2AM

H2A histone family, member N

NM_003514

h

3

    

Chromosome organization and biogenesis

HIST1H2BC

H2B histone family, member L

NM_003526

h

 

1

   

Chromosome organization and biogenesis

HIST1H2BD

H2B histone family, member B

NM_138720

hr

1

1

   

Chromosome organization and biogenesis

HIST1H2BJ

H2B histone family, member R

NM_021058

h

   

1

1

Chromosome organization and biogenesis

HIST1H2BL

H2B histone family, member C

NM_003519

h

1

    

Chromosome organization and biogenesis

HIST1H2BN

H2B histone family, member D

NM_003520

h

2

  

2

 

Chromosome organization and biogenesis

HIST2H2BE

H2B histone family, member Q

NM_003528

h

3

1

 

1

1

Chromosome organization and biogenesis

IGFBP2

Insulin-like growth factor binding protein 2 (36 kDa)

NM_000597

hmr

 

1 (hr)

  

4 (hmr)

Regulation of cell growth

LGALS3BP

Lectin, galactoside-binding, soluble, 3 binding protein

NM_005567

hmr

 

1

 

2 (hmr)

 

Cell adhesion

MATN2

Matrilin 2

NM_002380

h

1

    

Extracellular matrix assembly

MYST3

MYST histone acetyltransferase (monocytic leukemia) 3

NM_006766

hmr

 

5 (hmr)

  

6 (hmr)

DNA packaging

OLFM1

Olfactomedin 1

NM_014279

hmr

1

1

 

2

4 (hmr)

Morphogenesis

PRODH

Proline oxidase homolog

NM_016335

h

     

Amino acid metabolism

SLC9A3R1

Solute carrier family 9, isoform 3 regulatory factor 1

NM_004252

hmr

 

1

  

3 (hr)

Signal transduction

TDRD7

Tudor domain containing 7

NM_014290

hmr

1

1 (hmr)

  

5 (hmr)

Protein amino-terminus binding

TGM1

Transglutaminase 1

NM_000359

hmr

2

 

1

 

1

Morphogenesis; cell proliferation

THAP11

THAP domain containing 11

NM_020457

h

    

3

DNA binding, ion binding

UBADC1

Ubiquitin associated domain containing 1

NM_016172

hmr

2 (hmr)

   

7 (hmr)

Protein ubiquitination

XCL1

Chemokine (C motif) ligand 2

NM_002995

h

2

    

Signal transduction

XPA

Xeroderma pigmentosum, complementation group A

NM_000380

hmr

2

 

1

 

2 (hmr)

DNA repair

Cluster B

ABCG2

ATP-binding cassette, subfamily G (WHITE), member 2

NM_004827

h

 

3

1

 

2

Transport

ACSL5

Fatty-acid-coenzyme a ligase, long-chain 5

NM_016234

hmr

 

1 (hmr)

  

1

Fatty acid metabolism

AIF1

Allograft inflammatory factor 1

NM_001623

hmr

     

Inflammatory response; cell cycle

AKAP12

A kinase (PRKA) anchor protein (gravin) 12

NM_005100

hmr

1

2

  

2

Signal transduction

ARID3A

AT rich interactive domain 3A (BRIGHT-like)

NM_005224

hmr

2 (hmr)

1

  

3

Regulation of transcription

BCAT1

Branched chain aminotransferase 1, cytosolic

NM_005504

h

 

1

1

 

2

Cell cycle; amino acid metabolism

BIRC2

Baculoviral IAP repeat-containing 2

NM_001166

h

 

2

2

1

2

Antiapoptosis; signal transduction

CA9

Carbonic anhydrase IX

NM_001216

hmr

 

1 (hmr)

1 (hmr)

  

One-carbon compound metabolism

CAP2

Adenylyl cyclase-associated protein 2

NM_006366

hm

  

1

  

Signal transduction

CROC4

Transcriptional activator of the c-fos promoter

NM_006365

h

1

    

Cell proliferation

DMAP1

DNA methyltransferase 1-associated protein 1

NM_019100

hmr

 

3 (hr)

1

  

Regulation of transcription

DNAH11

Dynein, axonemal, heavy polypeptide 11

NM_003777

h

    

4

Transport

FADS3

Fatty acid desaturase 3

NM_021727

hmr

 

3

  

5 (hr)

Fatty acid metabolism

ICAM1

Intercellular adhesion molecule 1 (CD54)

NM_000201

hmr

 

2 (hmr)

1

1 (hmr)

3

Cell adhesion

IL6

Interleukin 6 (interferon, beta 2)

NM_000600

hmr

1 (hm)

1 (hmr)

1 (hmr)

 

1

Signal transduction; inflammatory response

IL8

Interleukin 8

NM_000584

h

 

1

1

1

 

Signal transduction; inflammatory response

KCNN4

Intermediate conductance Ca-activated K channel protein 1

NM_002250

hmr

1

3 (hmr)

1 (hmr)

  

Transport

KRT18

Keratin 18

NM_199187

h

1

1

   

Structural molecule activity

KRT8

Keratin 8

NM_002273

hr

2

2

1 (hr)

 

2

Structural molecule activity

MLPH

Melanophilin

NM_024101

h

 

1

  

2

Transport

Pfs2

DNA replication complex GINS protein PSF2

NM_016095

h

1

   

5

DNA metabolism

PLK1

Polo-like kinase (Drosophila)

NM_005030

hmr

 

1

 

1

1 (hm)

Metabolism; cell proliferation

PORIMIN

Pro-oncosis receptor inducing membrane injury gene

NM_052932

h

 

1

  

5

Oncosis-like cell death

PPP1R12A

Protein phosphatase 1, regulatory (inhibitor) subunit 12A

NM_002480

hmr

 

1

  

5 (hmr)

Regulation of organismal physiological process

PTPRJ

Protein tyrosine phosphatase, receptor type, J

NM_002843

h

 

1

  

8

Signal transduction

RAB17

RAB17, member RaS oncogene family

NM_022449

h

 

1

  

2

Signal transduction

RAD54L

RAD54-like (S. cerevisiae)

NM_003579

hmr

  

1

 

7

DNA repair; cell cycle

RPN2

Ribophorin II

NM_002951

hmr

 

1

1

1

1

Protein metabolism

SHANK2

Cortactin binding protein 1

NM_012309

hmr

 

2

 

2

4

Signal transduction

SNCG

Synuclein, gamma (breast cancer-specific protein 1)

NM_003087

hmr

    

1

Pathogenesis

SRPX2

Sushi-repeat protein

NM_014467

hmr

  

2 (hmr)

  

Electron transport

STC1

Stanniocalcin 1

NM_003155

hmr

1

  

3 (hmr)

 

Signal transduction

STK6

Serine/threonine kinase 15

NM_198433

hmr

   

1

 

Cell cycle

TOMM34

Translocase of outer mitochondrial membrane 34

NM_006809

hmr

 

3 (hmr)

  

2 (hmr)

Protein metabolism

TXNRD1

Thioredoxin reductase 1

NM_003330

hmr

 

1

2

 

1 (hmr)

Signal transduction

YAP1

Yes-associated protein 1, 65 kD

NM_006106

hmr

 

1

  

11(hmr)

Signal transduction

ZNF239

Zinc finger protein 239

NM_005674

h

   

1

 

Regulation of transcription

  1. Shown are numbers of transcription factor binding sites (TFBSs) from p53, nuclear factor-κB (NF-κB), activator protein (AP)-1, signal transducer and activator protein (STAT)3, and early growth response (EGR)1 in clusters A and B over-expressed in head and neck squamous cell carcinoma (HNSCC). TFBSs were predicted using Genomatix Suite 3.4.1 [108]. aOrthologous promoter sets are indicated by single-letter abbreviations (h, human; m, mouse; r, rat). bValues are presented as number of TFBSs in proximal region of promoters. The average length of these promoters was adjusted to approximately 600 base pairs (bp): about 500 bp upstream and about 100 bp downstream. Letters in the parentheses refer to conserved TFBSs identified among human, mouse, or rat using multiple sequence alignment of DiAlign TF of Genomatix Suite 3.4.1. cFrom Gene Ontology Annotation using Onto-Express [46], AmiGo [106], and National Center for Biotechnology Information [107]. TNF, tumor necrosis factor.