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The motif frequences for AT1G49720 (All Expression and Regulation tracks)

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Data last updated: 2018-03-03 09:40:09

Description

This track shows an example of motif frequencies of a transcription factor (TF) binding motif in corresponding genomic positions.

Methods

Given a TF binding site and corresponding binding motif, the motif frequency of each base pair was extracted according to genomic sequence.

Here is the TF binding motif matrix:

  A               C               G               T
  0.209830        0.073724        0.410208        0.306238
  0.659735        0.274102        0.024575        0.041588
  0.039698        0.831758        0.034026        0.094518
  1.000000        0.000000        0.000000        0.000000
  0.013233        0.954631        0.032136        0.000000
  0.022684        0.017013        0.943289        0.017013
  0.000000        0.052930        0.000000        0.947070
  0.000000        0.000000        1.000000        0.000000
  0.009452        0.017013        0.283554        0.689981
  0.083176        0.882798        0.000000        0.034026
  0.527410        0.107750        0.293006        0.071834

The corresponding genomic sequence (Chr1:8219814-8219824 +) is:

TACACGTGTCT

So the corresponding motif frequency of each base pair was highlighted below:

  A               C               G               T
  0.209830        0.073724        0.410208        0.306238
  0.659735        0.274102        0.024575        0.041588
  0.039698        0.831758        0.034026        0.094518
  1.000000        0.000000        0.000000        0.000000
  0.013233        0.954631        0.032136        0.000000
  0.022684        0.017013        0.943289        0.017013
  0.000000        0.052930        0.000000        0.947070
  0.000000        0.000000        1.000000        0.000000
  0.009452        0.017013        0.283554        0.689981
  0.083176        0.882798        0.000000        0.034026
  0.527410        0.107750        0.293006        0.071834

The extracted motif frequencies were:

0.306238, 0.659735, 0.831758, 1.000000, 0.954631, 0.943289, 0.947070, 1.000000, 0.689981, 0.882798, 0.071834

References

Jin, J., Tian, F., Yang, D. C., Meng, Y. Q., Kong, L., Luo, J., & Gao, G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res, 45(D1), D1040-D1045.