what is the meaning of "degenerative nature" of Chip-seq

Question

[pengchy]

In the paper [1], the following talk about the degenerative nature of "ChIP-seq" dataset. After a while googling, I still can not understand what is the meaning of "degenerative nature". Does it mean: Only part of the binding site were represented by the PWMs, there are still a large number of binding sites can not be detected by ChIP-Seq, so the scanning based on the PWMs should give more new TFBS. Isn't it?

Although the PWMs were derived from the corresponding ChIP-seq dataset, due to their degenerative nature, we still expected to obtain PWM hits that did not overlap with the ChIP-seq peaks.

[1] Gong, W., et al. (2015). "Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data." BMC Bioinformatics 16: 74.

Answer 1

[Fidel]

The sentence probably is not referring to the 'degenerative nature' of ChIP-seq but of motifs from which PWMs are derived. At least that's what I interpret. I think that what the authors want to say that is that PWMs obtained from ChIP peaks are expected to have hits even in regions not containing peaks. However, motif hits are expected elsewhere in the genome, besides ChIP peaks, for other reasons than their degenerative nature. For a recent review see: Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014). Absence of a simple code: how transcription factors read the genome. Trends in Biochemical Sciences, 39(9), 381-399. doi:10.1016/j.tibs.2014.07.002