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Table 2 The 19 features based on sequence and nearby gene expression

From: Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

No. Description Dir. P value Signif.
1 PhastCons score for 60-way vertebrate alignments; 0 if not available + 1.82E-09 ***
2 PhastCons score for placental mammal; 0 if not available + 7.76E-31 ***
3 1 if PhastCons vertebrate score is available and the score is 0; 0 otherwise + 1.55E-02 *
4 1 if PhastCons placental score is available and the score is 0; 0 otherwise - 4.53E-04 ***
5 1 if PhastCons vertebrate score is available; 0 otherwise + 7.24E-125 ***
6 1 if PhastCons placental score is available; 0 otherwise + 8.36E-01  
7 1 if base is in CpG islands; 0 otherwise + 1.03E-23 ***
8 ln(x + 5), where x is the absolute number of base pairs to nearest RefSeq transcription start site + 1.69E-02 *
9 1 if base is part of repeat element based on RepeatMaster; 0 otherwise - 6.07E-02  
10 1 if base is part of a transcribed region of a RefSeq gene; 0 otherwise - 2.76E-07 ***
11 1 if base is between the start and end of the coding region of the gene; 0 otherwise - 3.15E-05 ***
12 1 if base is part of RefSeq exon; 0 otherwise + 7.47E-03 **
13 1 if base is part of a RefSeq exon and within the coding region of the gene; 0 otherwise - 2.07E-105 ***
14 1 if base is part of a RefSeq intron; 0 otherwise + 2.19E-02 *
15 Percentage of G or C base pairs of all bases within 50 bases in either direction + 0.00E + 00 ***
16 ln(x + 1), where x is the FPKM of nearest gene at time t - 1.20E-07 ***
17 ln(x + 1), where x is the FPKM of nearest gene at time t + 1 + 3.81E-05 ***
18 1 if nearest gene is significantly up-regulated from t to t + 1; 0 otherwise + 2.05E-03 **
19 1 if nearest gene is significantly down-regulated from t to t + 1; 0 otherwise + 5.77E-02  
  1. *: 0.01≤p value < 0.05; **: 0.001≤p value < 0.01; ***: p value < 0.001.