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Table 3 Putative transcription factor models in 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

Model

Model matches in the cluster

% of matches in the clustera

% of hits in GPDb

Selectivityc

Selected genes from cluster Ad

   p53-TBPF

HIST1H2AM, HIST2H2BE, HIST1H2BL, HIST1H2BN, CPS1 , XPA, XCL1

41

4.39

9.4

   p53-TBPF-CREB

HIST1H2AM, HIST2H2BE, HIST1H2BL, CPS1, XCL1

29

0.68

43.3

   p53-TBPF-PCAT

HIST1H2AM, HIST2H2BE, HIST1H2BL, HIST1H2BN, CPS1

29

0.25

119.4

   p53-TBPF-CREB-TBPF

HIST1H2AM, HIST2H2BE, HIST1H2BL, CPS1, XCL1

29

0.19

151.8

   p53-TBPF-PCAT-SORY

HIST2H2BE, HIST1H2BL, HIST1H2BN, CPS1

24

0.02

1180.9

   p53-TBPF-CREB-ECAT

HIST1H2AM, HIST2H2BE, HIST1H2BL, CPS1

24

0.05

433.0

   p53-TBPF-VBPF-TBPF

HIST2H2BE, HIST1H2BL, CPS1, XCL1

24

0.06

371.1

   p53-TBPF-CREB-CDXF

HIST1H2AM, HIST2H2BE, HIST1H2BL, CPS1

24

0.04

541.2

Selected genes from cluster Be

   ETSF-NFκB

TOMM34 , DMAP1 , ACSL5 , YAP1, AKAP12, PLK1, TXNRD1, IL8, ABCG2, BIRC2, RAB17

42

17.21

2.5

   NFκB-ETSF

ICAM1 , DMAP1 , YAP1, RPN2, AKAP12, SHANK2, IL8, ABCG2, BIRC2, RAB17,

38

13.45

3.1

   ZBPF-NFκB

IL6 , ICAM1 , TOMM34 , KCNN4 , CA9 , FADS3, RPN2, SHANK2, ABCG2, RAB17

38

12.76

3.0

   EGRF-NFκBf

ICAM1 , TOMM34, CA9, DMAP1, FADS3, KRT8, ABCG2, MLPH,

31

15.71

2.0

   NFκB-EGRF(+)f

ICAM1 , KCNN4 , YAP1, FADS3, RPN2, AKAP12, TXNRD1, ABCG2

31

16.64

1.8

   NFκB-EGRF(-)f

ICAM1 , TOMM34 , FADS3, TXNRD1, ABCG2, MLPH, PORIMIN, PTPRJ

31

16.46

1.9

   NFκB-STATf

ICAM1 , TOMM34 , DMAP1 , FADS3, KRT 8, ABCG2, MLPH

27

9.57

2.8

   SP1-ZBPF-NFκB

IL6 , ICAM1 , KCNN4 , CA9 , FADS3, KRT8

23

4.02

5.7

   NFκB-ZBPF-EGRF

YAP1, TXND1, AKAP12, FADS3, PPP1R12A, RPN2

23

6.75

3.4

   ZBPF-NFκB-MAZF

KCNN4 , DMAP1 , YAP1, FADS3, TXNRD1, ABCG2

23

2.45

9.4

   NFκB-PAX5-ZBPF-ZBPFg

DMAP1 , TXNRD1, FADS3, ABCG2, BCAT1

19

1.46

13.2

   CREB-ZBPF-NFκB-ETSFg

IL6 , TOMM34 , KCNN4, ABCG2, PTPRJ

19

0.35

54.7

   NKXH-HOXF-CREB-NFκB-ETSFg

IL6 , TOMM34 , DMAP1, IL8

15

0.03

530.8

   HNF1-HOXF-CREB-NFκB-ETSFg

IL6 , TOMM34 , DMAP1, IL8

15

0.02

943.7

   EVI1-LHXF-HNF1-NFκB-ETSFg

ICAM1 , TOMM34 , DMAP1, IL8

15

0.01

1213.3

   NFκB-EGRF-ETSF-SP1F-ZBPFg

ICAM1 , TXNRD1, YAP1, ABCG2

15

0.22

70.8

   EVI1-HNF1-HOXF-NFκB-ETSFg

ICAM1 , TOMM34 , DMAP1, IL8

15

0.02

943.7

   EBOX-ZBPF-NFκB-MAZF-PAX5g

KCNN4 , YAP1, FADS3, ABCG2

15

0.13

116.3

  1. Shown are the selected models and their matches in the clusters A and B measured using FrameWorker, and hits in Genomatix promoter database (GPD) measured using ModelInspector of Genomatix Suite 3.4.1 [108]. In general, the distance between two transcription factor binding elements was limited to 5 to 150 base pairs. Genes in bold are orthologs; those in italic and bold contain conserved nuclear factor-κB (NF-κB) or p53 binding sites in orthologous promoter sets; underlined genes contain known NF-κB binding site. aPercentage of matches in p53 or NF-κB group in the cluster for that model. bPercentage of hits in all human promoters (55,207) in GPD for that model. cThe ratio between percentage of matches in the cluster and percentage of hits in the entire human promoters of GPD for that model [116]. dIncluding 17 input genes with predicted p53 binding sites in cluster A. p53 is shown in bold. eIncluding 26 input genes with predicted NF-κB binding sites in cluster B. NF-κB is shown in bold. fModel searching only covered five transcription factor families: NF-κB, p53, signal transducer and activator of transcription (STAT), activator protein (AP)-1, and early growth response family (EGRF). (-) and (+) indicate strand direction of EGRF binding sites. gThis distance was set to 5 to 200 base pairs.
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Genome Biology

ISSN: 1474-760X

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