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Table 6 The number of transcription factor binding sites correlated with the breadth of expression, the mean expression, and the median expression, but not with the value of the maximum expression of a transcript

From: A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators

Expression feature

The strength of correlation Tfbs No.

t a

df b

P-valuec

Breadth at the cutoff of 10 TPM

r p  = 0.448

t = 88.1194

df = 30873

< 2.2e-16

Breadth at the cutoff of 100 TPM

r p  = 0.16

t = 28.6497

df = 30873

< 2.2e-16

Breadth at the cutoff of 1,000 TPM

r p  = 0.035

t = 6.1749

df = 30873

6.70E-10

Mean expression

r p  = 0.13

t = 23.3451

df = 30873

< 2.2e-16

Median expression

r p  = 0.254

t = 46.2675

df = 30873

< 2.2e-16

Maximum expression

r p  = −0.02

t = −3.5161

df = 30873

0.00043

Breadth-conditioned-mean expression

r p  = −0.041

t = −6.4983

df = 25040

8.277e-11

Breadth-conditioned-median expression

r p  = −0.026

t = −4.1194

df = 25040

3.811e-05

  1. Here the mean/median were defined across all samples even if the expression level was zero. As this forces a necessary correlation with breadth, we repeated the same using mean/median defined only for samples where expression is seen (breadth-conditioned-mean and median expression).
  2. NOTE: TPM stands for “tags per million”. The TPM value of ten was accepted as the standard threshold for a gene to be “on” in a given library. The breadth of expression was the fraction of samples in which the gene was “on”. 10 TPM corresponded to ~3 mRNA copies per cell based on 300,000 mRNAs/cell [[28]].
  3. at-statistic.
  4. b degrees of freedom.
  5. c number of data-points.