Question: Cell Line/Tissue Comparison between Fantom5 and Roadmap
1
gravatar for jesselee516
3.3 years ago by
jesselee51690
United States
jesselee51690 wrote:

Hi everyone,

Have you ever compared the tissue/cell line between Fantom5 and roadmap. What I need is how many of roadmap cell line/Tissue are coverd in Fantom5. And what is most importly is, for each cell line/tissue in roadmap, which one is exactly corresponding cell line/tissue in Fantom5? What I mean is how to match cell line/tissue beteen these two.

 

Thanks very mcuh...

roadmap encode fantom5 • 1.2k views
ADD COMMENTlink modified 3.3 years ago by muralinmars70 • written 3.3 years ago by jesselee51690
0
gravatar for Giovanni M Dall'Olio
3.3 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

I know, it's very complicated to compare ENCODE because for some reasons they use different cell lines ids.

I am not aware of any formal comparison table, but you can get the list of FANTOM cell lines from here: http://fantom.gsc.riken.jp/5/datafiles/latest/basic/ (HumanSamples2.0.sdrf.xlsx) and the ENCODE lines from here: https://genome.ucsc.edu/ENCODE/cellTypes.html

 

ADD COMMENTlink written 3.3 years ago by Giovanni M Dall'Olio26k
0
gravatar for muralinmars
3.3 years ago by
muralinmars70
France
muralinmars70 wrote:

I have learnt that the roadmap and Fantom cover different aspects. Roadmap - epigenomes (primarily) and Fantom (TFs). Curious to know the objective behind comparing these two datasets.

Thanks

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by muralinmars70
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