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Table 2 Comparison of nuclear and cytoplasmic chromosomes.

From: ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data

  

Total Reads

Chr

 

In ChIP

In input

ChIP/input ratio

 

Specific Reads

2356286

441471

5.3373

1-22, X

Noise Reads

24285371

22585024

1.0753

 

E(background

4959671

  
 

noise) in ChIP*

(0.2042)

  

M

 

89835

409136

0.2196

  1. *Assuming that reads mapped to mitochondrial chromosomes (M) are due to the experimental procedure and not to the non-specific binding of STAT1, the ChIP/input ratio for this background noise is 21.96%. Among chromosome 1-22 and X, the expected background noise in ChIP would be 22585024*0.2196 = 4959671, which accounts for 20.42% of total noise reads.
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Theoretical Biology and Medical Modelling

ISSN: 1742-4682