Table 3

Putative transcription factor models in clusters A and B over-expressed in HNSCC

Model

Model matches in the cluster

% of matches in the cluster^a

% of hits in GPD^b

Selectivity^c

Selected genes from cluster A^d

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 B^e

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-NFκB^f

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-STAT^f

ICAM1, TOMM34, DMAP1, FADS3, KRT8, 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-ZBPF^g

DMAP1, TXNRD1, FADS3, ABCG2, BCAT1

19

1.46

13.2

CREB-ZBPF-NFκB-ETSF^g

IL6, TOMM34, KCNN4, ABCG2, PTPRJ

19

0.35

54.7

NKXH-HOXF-CREB-NFκB-ETSF^g

IL6, TOMM34, DMAP1, IL8

15

0.03

530.8

HNF1-HOXF-CREB-NFκB-ETSF^g

IL6, TOMM34, DMAP1, IL8

15

0.02

943.7

EVI1-LHXF-HNF1-NFκB-ETSF^g

ICAM1, TOMM34, DMAP1, IL8

15

0.01

1213.3

NFκB-EGRF-ETSF-SP1F-ZBPF^g

ICAM1, TXNRD1, YAP1, ABCG2

15

0.22

70.8

EVI1-HNF1-HOXF-NFκB-ETSF^g

ICAM1, TOMM34, DMAP1, IL8

15

0.02

943.7

EBOX-ZBPF-NFκB-MAZF-PAX5^g

KCNN4, YAP1, FADS3, ABCG2

15

0.13

116.3

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.

Yan et al. Genome Biology 2007 8:R78   doi:10.1186/gb-2007-8-5-r78