Question about ChromHMM overlap enrichment
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3.2 years ago
nanoide ▴ 70

Hello, I've used ChromHMM with ChIP-seq aligment and identified some chromatin states of itnerest.

I am interested in the overlapping with other datasets to annotate them according to the segment they are located on. OverlapEnrichment seems exactly what I'm looking for, but I think I'm failing to interpret it correctly.

Running LearnModel with Chip-Seq aligments of two conditions, I get the expected segmentation (guess with staes based on both conditions). I then get two overlap enrichment plots, one per condition, for the dataset of regions I have provided. I have then overlapped using bedtools intersect the segmentation provided for each condition with my dataste of regions. The overlaps I'm getting don't make sense compared to the enrichment plots. For example, more than half of my regions overlap with a segment which is not enriched according to the figure.

Maybe I'm missing something, I'm asking in case someone has any experience. How could I get the segments corresponding to each region on my dataset?

Hope anyone has any comment on this. Thanks

ChromHMM ChIP-Seq segmentation • 1.5k views
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Hi @nanoide, Even I am trying to do something similar. Was just curious to ask were you able to get the answers what you were looking for? I'll appreciate if you can share your experience here and the strategy you followed to get this done.

Thanks

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"For example, more than half of my regions overlap with a segment which is not enriched according to the figure." By segment, do you mean state? The enrichment is based on the expected overlap of the states with the regions of interest assuming the null hypothesis. In other words, if a state is predicted at 25% of your genome, then by random chance you would expect it to cover 25% of any regions of interest, so it would need to show significantly more than 25% coverage to be considered enriched for those regions.

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