I am characterizing the function of a DNA binding protein along cell differentiation. ChIP-seq. has been conducted. Since my ChIP-seq. datasets are from 3 differential time points, differential enrichment of the protein was called for further studies. My goal is to suggest if the differential enrichment of my protein plays activator or repressor role to particular pathways or processes.
e.g. Input: Time point 1 unique peaks (The peak only presence in time point 1 but not time point 2 and 3: My protein is loss from this sites during cell differentiation) for gene ontology (using GREAT, http://great.stanford.edu/). Output: A list of GO terms as shown in the image below.
My questions: 1. There is a term called "regulation of stem cell differentiation". How do I know my protein is positively or negatively regulating stem cell differentiation? 2. For terms like "Placenta development", how can I know if my protein promotes or represses this process?
* I know it would be easier to combine ChIP-seq. and gene expression data to predict if the protein of interest is a positive or negative regulator. However, the majority of peaks from my datasets are intergenic and enhancer datasets are lacking for this cell type. I cannot answer the questions by looking at gene expression data. *
Any suggestions are welcome and appreciated. Thanks!