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Table 1 Motif associated with histological grades or prognosis identified based on independent datasets

From: Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells

  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
  1. 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.
  2. bThe number of appearances of sequence feature in 30 searches with bootstrap resampling.
  3. cdP values calculated by Wilcoxon rank sum tests for training and test data, respectively.
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