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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

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