Cell Line/Tissue Comparison between Fantom5 and Roadmap
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6.0 years ago
jesselee516 ▴ 100

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...

fantom5 roadmap encode • 1.8k views
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6.0 years ago

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

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5.9 years ago
muralinmars ▴ 100

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

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