I have set of differentially expressed gene files. I need to figure out if a specific histone is associated with changes in their promoters.
Is there a specific galaxy tool similar to annotation hub in R available.
Please suggest
I have set of differentially expressed gene files. I need to figure out if a specific histone is associated with changes in their promoters.
Is there a specific galaxy tool similar to annotation hub in R available.
Please suggest
Try the tool: AnnotateMyIDs (a function from Bioconductor’s R AnnotationHub) to see if that contains the data you want. See the supported organisms on the tool form.
To access more R functions, or those not specifically wrapped by a tool, try: Visualize > Interactive Environments.
Thanks a ton , this was very helpful
This helped me to annotate my gene, but which tool I used to get the epigenetic peaks . Please suggets
The question is a bit broad with the given info, but how to get, produce, analyze epigenetic data (are many types!) depends on your organism, data providers that support it (for pre-computed or raw data eg: ENCODE and others), what kind of data you already have or decide to link in, the tools that will work with it, larger goals.
Tips:
Very simple answer with many assumptions, as an example, that can all be done within Galaxy.
For a human gene list or genome coordinates of regions of interest for those genes: review the UCSC > ENCODE data tracks. The raw data is available for use in peak calling tools plus they have a few tracks specific to histone markers targeted at promoters and other regulatory elements. Peaks (generated by them, or by you from the raw data) could then be compared to genes/genomic coordinates/regulatory regions of interest. Up/down-expression overlapping with marker peaks could then be investigated with a tool suites like DeepTools and HiCExplorer.
Thank you so much. Your knowledge is awesome.