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Table 4 Results oPOSSUM analysis of overrepresented transcription factors in the differentially expressed genes from limma (logFC > 0.5, FDR < 0.01)

From: Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients

TF

TF class

Target genes

Z-scorea

Fisher scoreb

SCC vs NS

    

Up- and downregulated genes (1514 of 2036 genes included c )

SRF

MADS

107

12.25

7.38E-05

Hand1-Tcfe2a

bHLH

1148

10.30

3.31E-06

RELA

REL

576

8.01

1.21E-06

SP1

ZN-FINGER, C2H2

1036

7.80

1.34E-09

SPIB

ETS

1374

5.97

4.72E-06

Upregulated genes (736 of 1039 genes included)

  

SRF

MADS

62

16.93

5.02E-05

RELA

REL

291

11.68

2.66E-04

Hand1-Tcfe2a

bHLH

565

9.30

1.53E-02

ELF5

ETS

658

9.25

2.38E-05

REL

REL

450

8.40

2.86E-05

Downregulated genes (758 of 1004 genes included)

FOXF2

FORKHEAD

221

12.93

1.52E-06

SP1

ZN-FINGER, C2H2

536

11.03

1.12E-08

FOXD1

FORKHEAD

459

8.409

2.16E-06

Foxq1

FORKHEAD

349

7.176

1.47E-06

TP53

P53

3

6.687

1.04E-01

AK vs NS

    

Up- and downregulated genes (695 of 960 genes included)

SP1

ZN-FINGER, C2H2

494

16.58

1.32E-08

MZF1_1-4

ZN-FINGER, C2H2

644

14.28

2.43E-07

SRF

MADS

56

13.50

1.32E-04

Cebpa

bZIP

437

10.90

1.99E-05

TEAD1

TEA

217

10.80

8.74E-05

MZF1_5-13

ZN-FINGER, C2H2

527

10.37

1.59E-08

Upregulated genes (364 of 515 genes included)

  

SRF

MADS

35

19.82

8.10E-05

ELF5

ETS

319

11.05

2.04E-04

RELA

REL

150

10.03

1.60E-04

SPIB

ETS

338

9.25

2.28E-04

TLX1-NFIC

HOMEO/CAAT

32

9.00

5.07E-03

Downregulated genes (695 of 960 genes included)

  

SP1

ZN-FINGER, C2H2

248

17.04

1.63E-07

MZF1_1-4

ZN-FINGER, C2H2

309

11.7

3.74E-04

Arnt-Ahr

bHLH

289

11.49

2.25E-09

Cebpa

bZIP

228

11.18

5.86E-07

Roaz

ZN-FINGER, C2H2

130

10.88

2.11E-05

SCC vs AK

    

Up- and downregulated genes (412 of 553 genes included)

RREB1

ZN-FINGER, C2H2

38

11.29

1.24E-03

FOXF2

FORKHEAD

111

10.99

7.16E-03

SRF

MADS

36

10.01

4.10E-04

RELA

REL

163

9.239

8.26E-04

TEAD1

TEA

120

8.031

2.46E-02

Upregulated genes (209 of 283 genes included)

  

SRF

MADS

24

15.39

6.72E-05

RELA

REL

85

11.99

5.32E-03

Fos

bZIP

157

10.98

3.68E-04

NF-kappaB

REL

108

8.39

2.22E-04

REL

REL

129

7.91

1.93E-03

Downregulated genes (204 of 271 genes included)

  

FOXF2

FORKHEAD

70

22.37

2.55E-05

FOXI1

FORKHEAD

126

10.74

7.22E-02

RREB1

ZN-FINGER, C2H2

22

9.86

1.81E-03

T

T-BOX

28

8.77

5.00E-03

Foxd3

FORKHEAD

129

7.91

5.37E-02

Progression genes

    

Up- and downregulated genes (128 of 172 genes included)

RELA

REL

54

10.18

1.00E-02

SP1

ZN-FINGER, C2H2

94

9.66

1.76E-03

FOXF2

FORKHEAD

36

7.30

5.18E-02

NFKB1

REL

35

6.21

1.09E-02

MZF1_1-4

ZN-FINGER, C2H2

118

6.11

3.15E-02

Upregulated genes (53 of 85 genes included)

  

RELA

REL

23

14.0

5.41E-02

NFKB1

REL

19

9.78

2.48E-03

SRF

MADS

6

8.09

3.82E-02

TLX1-NFIC

HOMEO/CAAT

7

7.65

2.27E-02

MIZF

ZN-FINGER, C2H2

11

7.11

3.21E-02

Downregulated genes (75 of 87 genes included)

  

FOXF2

FORKHEAD

29

14.63

6.46E-04

FOXI1

FORKHEAD

48

11.42

1.14E-01

T

T-BOX

13

8.14

7.45E-03

Foxa2

FORKHEAD

50

8.02

4.40E-02

SP1

ZN-FINGER, C2H2

56

7.60

7.94E-03

  1. a The Z-score determines whether a TFBS occurs more frequently in the set of co-expressed genes compared to pre-computed background set provided by the package.
  2. b The Fisher score (one-tailed Fisher exact) is calculated to determine the probability of non-random association between the co-expressed genes and the TFBS site of interest.
  3. c The number of genes in the differentially expressed gene set that could be aligned to the pre-computed background.
  4. For more details on the oPOSSUM analysis: S.J. Ho Sui et al., (2005) Nucleic Acid Res., 33: 3154–64.
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BMC Cancer

ISSN: 1471-2407

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