Is there a way to extract tissue specific genes from efp browser in bulk?

Question

[ktm]

I am interested in genes active in different root tissues. When I have a gene I can look at the EFP browser on arabidopsis.org and find in what tissue of the root it is being expressed. Is there a way to do it the other way around? Or a way to retrieve this information in bulk?

[i.sudbery]

I don't know the arabidopsis resources well enough I expect not, as no two people will agree on a meaning of "tissue specific".

Answer 1

[nicholas.provart]

Hi KTM, why yes, there is! We provide those eFP images to TAIR - and we have a tool called Expression Angler where you can design a "bait" i.e. guide vector that is specific for a given tissue/sample in a given compendium - see Figure 1 of this paper: https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.13261 ...hope this helps. Nick

Answer 2

[nicholas.provart]

P.s. you can use an older version of the Expression Angler interface and search in our large root compendium for region-specific genes: http://bar.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=expt_select (choose Root Compendium then tick off the samples you want to search in and enter 1s for low expression and 100s for high expression). Best, Nick