Ingenuity Pathway Analysis Galaxy Dataset

Question

[benjyrolls]

Hi

I have a MACS output from a ChIP-Seq experiment, could someone explain how I can find the processes which are down or up regulated using my peaks interval file.

I have used GREAT but am only able to find genes and a few processes which are enriched.

Secondly I have Ingenuity Pathway Analysis how can I use my MACS output to find processes which are down or upregulated in both IPA and GREAT?

Thanks

Benjy

Answer 1

[EagleEye]

Simple and ideal thing will be,

1) Assign your positive and negative peaks regions to genes.

2) Use those two gene list in gene enrichment analysis tools like GeneSCF.

[benjyrolls]

Thanks for the Reply.

I have these output from MACS2.1

1. (treat pileup: bedGraph)
2. (peaks: interval)
3. (peaks: narrowPeak)
4. (summits: bed)
5. (control lambda: bedGraph)
6. (treat pileup: bigWig)

so I havent got the negative and positive peaks. How do I get these negative and positive peaks(sorry am a bit new to this) ?

[EagleEye]

It looks like MACSv2 does not provide output with 'negative peaks' like it was in MACSv1. In that case I assume you switch your control and treatment samples to get negative peaks.

[benjyrolls]

Thanks I have the negative and positive peaks now. Is it advisable to add some bases to the left and right from the peaks summits file, as its normally done in discovering motiffs, which files to use here the peaks interval for GeneSCF? MACS2 provides gene ids in RefSeq form? Will GeneSCF work on Windows 7?

[EagleEye]

Hi,

You can also use GREAT to associate your peaks to genes. GREAT will give you output with associated gene symbols to individual peaks. Those gene symbols can be used in GeneSCF to get enriched terms or biological process.

Note: GeneSCF only works on Linux system, it has been successfully tested on Ubuntu, Mint and Cent OS. Other distributions of Linux might work as well. Recently we have also successfully tested GeneSCF v1.1 on Windows 10 (bash 1607).

I am the author/developer of GeneSCF, that's the reason why I am insisting you to use it. But you can use whatever tool is convenient for you with your obtained gene symbols. You should also consider the advantages of using GeneSCF. If you have any difficulties in using GeneSCF, please post a question in Biostars to get quick response.