Cell Line/Tissue Comparison between Fantom5 and Roadmap

Question

[jesselee516]

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.

Answer 1

[Giovanni M Dall'Olio]

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

Answer 2

[muralinmars]

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