What’s the Answer? (FANTOM5 promoter atlas)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

This week’s highlighted question at Biostar is something that rang a bell. I’ve been meaning to take a look at this resource, but it got buried on my desk under a pile of other stuff and I forgot to get back to it.

Question: FANTOM5 Promoter Atlas

Hi All,

I went through this paper on promoter atlas in FANTOM5 http://www.nature.com/nature/journal/v507/n7493/full/nature13182.html#the-fantom5-promoter-atlas , my question is that do they have cell wise CAGE dataset or is it global , as I cannot see the cell wise CAGE expression on their website.

Thanks in advance.


The thing that reminded me about that paper was in the answer–Taylor Raborn noted that this can be found in the ZENBU resources. In both March and in May I started tip-of-the-week posts about ZENBU as I can tell from my draft folder, but other stuff came up. I really have to visit that in the new year. If people could stop developing new resources for a while, I can catch up…? Right, that will happen.

Until I have a chance to get back to it (we have our annual special summary posts over the next two weeks and other stuff already in the hopper for early next year), you’ll have to settle for the ZENBU wiki details on their genome browser.

Forrest A.R.R., Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh & Robin Andersson & (2014). A promoter-level mammalian expression atlas, Nature, 507 (7493) 462-470. DOI: http://dx.doi.org/10.1038/nature13182

Severin J., Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, Nicolas Bertin & Alistair R R Forrest (2014). Interactive visualization and analysis of large-scale sequencing datasets using ZENBU, Nature Biotechnology, 32 (3) 217-219. DOI: http://dx.doi.org/10.1038/nbt.2840