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Cell Line/Tissue Comparison between Fantom5 and Roadmap

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 covered in Fantom5. And what is most important 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 between these two.

Thanks very much.

encode fantom5 roadmap
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updated by Ram Ram • written by jesselee516 jesselee516

2 answers

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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updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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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written by muralinmars • muralinmars

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