Table 1

Motif associated with histological grades or prognosis identified based on independent datasets

^aMotif ID

^bReproducibility

^cP value for training data

^dP value for test data

JSP$NF_Y(20)

20

3.1 × 10^-10

0.000158

V$NRF1_Q6(10)

15

3.09 × 10^-14

6.02 × 10^-7

motifs associated with histological grades based on the data by Sotiriou et al.

V$ELK1_02(20)

12

9.25 × 10^-26

1.41 × 10^-6

DME$CTTCCGSYN(5)

9

5.71 × 10^-14

6.82 × 10^-5

V$E2F1_Q4_01(5)

7

5.71 × 10^-15

0.002372

JSP$NF_Y(10)

15

2.46 × 10^-14

0.011049

DME$RMSYSSARGCGC(5)

11

4.02 × 10^-5

0.063412

V$ELK1_02(10)

10

2.03 × 10^-16

2.08 × 10^-7

motifs associated with prognosis based on the data by Sotiriou et al.

DME$YYYGSGCMYGCG(5)

8

1.65 × 10^-9

0.008054

V$E2F1_Q4_01(10)

8

1.05 × 10^-17

2.37 × 10^-5

V$IRF_Q6_01(10)

7

2.06 × 10^-8

0.000152

DME$NMSTTCYKSYR(5)

6

0.000669

0.084446

V$NRF1_Q6(20)

6

9.02 × 10^-22

1.31 × 10^-6

JSP$NF_Y(20)

22

5.93 × 10^-8

0.01116

motifs associated with histological grades based on the data by Pawitan et al.

V$E2F1_Q4_01(5)

10

6.56 × 10^-7

0.049423

DME$RCRKGCGCAVN(5)

6

5.71 × 10^-8

0.060899

V$E2F1_Q4_01(15)

6

9.59 × 10^-6

0.017285

V$ELK1_02(20)

16

1.26 × 10^-27

6.13 × 10^-12

V$NRF1_Q6(15)

11

9.2 × 10^-23

3.89 × 10^-7

motifs associated with prognosis based on the data by Pawitan et al.

V$NRF1_Q6(20)

11

4.31 × 10^-22

2.49 × 10^-7

V$ELK1_02(15)

9

1.63 × 10^-25

6.41 × 10^-11

DME$RCGCHKGCGY(5)

6

3.23 × 10^-20

4.8 × 10^-6

^aIDs starting from "V$", "JSP$", and "DME$" Motifs denote motifs from the TRANSFAC database, the JASPAR database, and our DME analysis, respectively, followed by values of the threshold parameter for motif searches in parentheses.

^bThe number of appearances of sequence feature in 30 searches with bootstrap resampling.

^cdP values calculated by Wilcoxon rank sum tests for training and test data, respectively.

Niida et al. BMC Bioinformatics 2008 9:404   doi:10.1186/1471-2105-9-404