how the chip-seq is represented?

Question

[maria]

Hi, A microarray data can be represented by a matrix (lines:genes, columns: samples), but how the chip-seq data are represented by a matrix? I have to know wich transcription factors regulate wich groupe of genes, so I should analyze the chip-seq, chip-chip or the microarray ?

[Lila M]

You could perform the annotation and after that represent the TSS profile. There are a lot of tools that may help you, start wit homer, deepTools, bioconductor (ChiPseeker...), but you need to resolve first more basics questions of interest :)

[maria]

ths you Lila, first it is necessery to classify genes according to their similarity of expressions profiles, these genes are likely to be regulated via the same mechanisms so will be bound by the same TFs?

[Devon Ryan]

Like all other questions in science, you can answer this by answering all intermediate questions first. In this case, the first intermediate question is, "how does one determine whether a gene is regulated by a transcription factor?", followed by "what would be needed for a gene to regulate a transcription factor?". Answer the intermediate questions first and then you can ask a more concrete question that better fits in the purview of the site.