<p>For a given cell line, I have ChIP-seq and RNA-seq data. I am trying to construct a model for predicting gene expression from ChIP-seq. Basic  models  I have seen [a very simple model is described in  https://www.pnas.org/doi/10.1073/pnas.0904863106 ] generally rely on chip-peak-to-gene-distance:</p>
<p>Gene_Expression(gene)=F_gene(ChIP-Type,tag_count,distance_to_gene)</p>
<p>This peak to gene distance dependence seems over-simplified, so I am looking for alternative, possibly more nuanced, quantitative models to describe ChiP (TF) to gene expression dependence.</p>

CC BY-SA 4.0
2024-05-27T07:24:29.763Z
I predict that this question will receive many "needs more focus" votes. The entire problem of peak to gene association is very unsolved. There is reviews that summarize the different approaches that have been developed over the last two decades. Please read them first, and then ask a precise technical question.
ATpoint
CC BY-SA 4.0
2024-06-01T19:15:31.270Z
Thank you @ATpoint, I recognize  the question is posed generally - and that is somewhat the point here - that you've touched on with your "very unsolved" characterization. What I have seen, in the few articles I have read, are arbitrary specialization of  models without satisfactory justification - getting the sense of a struggle to formalize the variations of functional connection types between Gene expression and regulatory elements/signals. For this reason I am looking for broader/general input.
Zebra Fish
<rna-seq><chip-seq><hi-c>
Predicting gene expression, RNA-seq, from regulatory signals, ChIP-seq
# Predicting gene expression, RNA-seq, from regulatory signals, ChIP-seq

(Asked by: username_0 on 2024-05-26)

For a given cell line, I have ChIP-seq and RNA-seq data. I am trying to construct a model for predicting gene expression from ChIP-seq. Basic models I have seen [a very simple model is described in https://www.pnas.org/doi/10.1073/pnas.0904863106 ] generally rely on chip-peak-to-gene-distance:

Gene\_Expression(gene)=F\_gene(ChIP-Type,tag\_count,distance\_to\_gene)

This peak to gene distance dependence seems over-simplified, so I am looking for alternative, possibly more nuanced, quantitative models to describe ChiP (TF) to gene expression dependence.

**Tags:** rna-seq, chip-seq, hi-c
> **Comments:**
> **username_1**: I predict that this question will receive many "needs more focus" votes. The entire problem of peak to gene association is very unsolved. There is reviews that summarize the different approaches that have been developed over the last two decades. Please read them first, and then ask a precise technical question.  
> **username_0**: Thank you @ATpoint, I recognize  the question is posed generally - and that is somewhat the point here - that you've touched on with your "very unsolved" characterization. What I have seen, in the few articles I have read, are arbitrary specialization of  models without satisfactory justification - getting the sense of a struggle to formalize the variations of functional connection types between Gene expression and regulatory elements/signals. For this reason I am looking for broader/general input.  

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