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PostPosted: Mon Sep 09, 2013 9:58 pm 
Hi,
I'm fairly new to using GREAT in analyzing my ChIPseq data. Are the terms that are generated from the Pathway Commons or MSigDB perturbations determined from my gene list (which can vary depending on how I set my region-gene association settings) or from the actual regions? For example, one of the terms in my MSigDB Perturbation list is "Set 'Myc targets1': targets of c-Myc [Gene ID=4609] identified by ChIP on chip in cultured cell lines, focusing on E-box???containing genes; high affinity bound subset". Does this mean that this term popped up as a significant term b/c my regions corresponds to the regions determined by the MSigDB's ChIP on chip sequences? or is it b/c my gene list is similar to their gene list?
Thanks!
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PostPosted: Mon Sep 09, 2013 10:30 pm 
Site Admin
> Are the terms that are generated from the Pathway Commons or MSigDB perturbations determined from my gene
> list (which can vary depending on how I set my region-gene association settings) or from the actual regions?

The significance of a particular term is determined by the region-gene association settings AND the actual regions since the statistical test (http://great.stanford.edu/help/display/GREAT/Statistics) computes the significance of your set of regions falling in the regulatory domains (defined by the region-gene association settings) of genes involved in a particular function compared to random.

> Does this mean that this term popped up as a significant term b/c my regions corresponds to the
> regions determined by the MSigDB's ChIP on chip sequences? or is it b/c my gene list is similar to their gene list?

The term is significant because significantly more regions in your set are fall in the regulatory domains of those genes and thus GREAT is hypothesizing that your regions are involved in the regulation of those genes. One point to note is that your regions may be completely different than those regions that were used by MSigDB to determine those genes as c-Myc targets. The enrichment should be read as have a set that is enriched in the regulation of c-Myc targets.

Thanks,
Bejerano Team
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 Post subject: Thanks!
PostPosted: Mon Sep 09, 2013 10:34 pm 
Thanks! That was very helpful!
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