I have a set of genomic regions, about 8000 intervals, and I'd like to
them by expression in certain tissues - does anyone know if that is
possible? I am not having much luck in UCSC determining which track of
corresponds to a certain tissue. For example - I would like to filter
only those expressed in lymphoctyes (which may mean combining on
fields - whole blood, T cells, B cells, monocytes).
Any insight or suggestions would be appreciated.
For hg18, the full compliment of ENCODE experiments plus other
expression data is available in the track group "Expression" at UCSC.
Exploring the contents of these through the UCSC Browser's Gene Sorter
or track description pages (click on track names) is advised. For
detailed help, contacting UCSC directly (firstname.lastname@example.org) for help
regarding which exact track/tables would be recommended. There are
choices and most will require some subjective stringency filtering.
Also, since much of the data is normalized in the schema and will
require file merges to create the final reference file, they can help
you navigate to which tables are most important for your particular
Once the tracks & tables are identified, move the data into Galaxy
"Get data -> Bx Main" with the Table browser (a mirror of the UCSC
browser that will allow you to load larger files, the UCSC Table
has a transfer limit at ~ 100k lines). Merge/format/filter as needed
using the tools in "Text manipulation", load your intervals "Get data
Upload File", and use the Interval comparison tools to perform the
analysis. Save as a workflow to use the analysis path multiple times
(useful as you work through the process of tuning parameters, reuse
future experiments, etc.).
We know that UCSC is in the process of mapping ENCODE onto the hg19
genome, but that project is not completed yet. Currently there are
two expression tracks available and I don't think they will address
question, but it is worth a look. This is another question you could
them about if hg19 is your ultimate target.
Sorry that we could not specifically help with the data part of your
question - expression data usually requires complex data reduction
methods - and the ENCODE experts are the best qualified folks to offer
help. But, we can certainly offer more help with Galaxy's tools once
have that part settled. Please let us know if we can assist you
during the analysis phase of your project.