integration analysis of multiple ChIP-seq (TFBS or histone from ENCODE)

Question

[xfliwz]

Hello, I am interested in system analysis ChIP-seq data (tfbs or histone). I wonder if I have several ChIP-seq data sets of transcription factors (TF) and histone modification, how can I integrate those ChIP-seq data information to uncover the under relationship of those TF or histone? Any suggestion will be welcome!

Answer 1

[Emily]

We have carried out these kinds of analyses at Ensembl to identify the functions of different genomic regions. You can learn more about how we did this here and look at our data here.

[xfliwz]

Thanks for your answer! It is very useful. ChromHMM is a powerful tools to do integrated analysis ChIP-seq data. You know that the parameter of state is user-defined. How could I know the value of state is suitable for my own data sets?