Tool to predict Enhancer gene target
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4.1 years ago

Hello guys!

I'm starting to work on a list of putative enhancers. I'd like to understand what are the putative targets of this enhancers.Do you have any suggestions on what tool I can use? I'm working on primary mouse Mesenchimal Stem Cells (kind of).

Thanks! Luca

ChIP-Seq • 1.9k views
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4.1 years ago

Finding gene targets of putative regulatory elements is always a challenge. Common methods range from simply assigning them to the nearest gene (not all that accurate, but certainly the easiest), to trying to corroborate their "activity" with expression of nearby genes in the same sample, to integrating chromatin interaction data (ala Hi-C/ChIA-PET/5C-based methods) to identify topologically associated domains since most enhancers only regulate genes within their respective TAD.

Depending on what data you have available or can find publicly, you can try a few different methods. ChIPseeker is a decent R package that will assign your enhancers to the nearest genes and is useful for generating some decent summary figures. It can also be integrated with clusterProfiler for GO/pathway enrichment analyses. GREAT is another tool in the same vein, but completely web-based.

As for the other options, you'll have to write something in R or Python to pull out potential targets for each enhancer. I don't know of any tools that tie in expression or interactome data off the top of my head, though they may very well exist.

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Actually GREAT now has an R package associated with it, which I find much more useful than the web interface.

[https://bioconductor.org/packages/release/bioc/html/rGREAT.html][1]

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Oh, that's very good to know, as using the web interface was definitely a drawback compared to the other options.

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Thanks Jared to always answer my questions! It's very well appreciated. (I have a list of enhancers also thanks to your reply in the other post 😂).

I'll have a look at the tools you are suggesting, for now I'm using http://www.enhanceratlas.org. It uses some list of already annotated Enhancer-Promoter regulation. Do you think is a viable strategy?

Data at my disposal are: H3k9-14ac H3k27ac NAseq RNAseq

My (naive I guess) strategy would be to take those annotated enhancer and see the modulation via RNAseq.

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I thought your data was for arabidopsis? EnhancerAtlas only has human tissues, so be aware of that.

The GeneHancer UCSC track is kind of my favorite for this sort of thing because it integrates a bunch of different data sources and takes an approach that I really appreciate, but again, it's only for human data.

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What a shame is just for Human Data... Actually my data are in Mouse!

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Ah, then mouse ENCODE might be helpful for you. You can also check out the WashU Epigenome browser, as it has a lot of regulation/epigenomic data as well. GREAT/clusterProfiler will also still work fine for mouse data.

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Thank you so much for all the help and suggestions 😊

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Jared - I know this is late, but do you know where I can download the GeneHancer table? I see the track hub on UCSC, but I'd like to use the database itself for some analyses in R if possible, but I can't find a download anywhere?

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The UCSC Table Browser lets you download the data behind pretty much any track available to you. For GeneHancer, change Group to Regulation, then select GeneHancer from the Track dropdown. Stick in an output file name, click get output, and you should be set.

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Wow I'm not sure how I didn't try that before, but thank you for that quick and easy answer!

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