Retrieve tissue expression in Zfin (R/python)

Question

[A. Domingues]

In zfin it is possible to find in which tissue/developmental stage a gene is expressed. The question is:

Is there a way of querying the database for this information using R/Python/bash?

I naively assumed that someone would have added that information as a bioconductor package. but could not find it.

[teresa.noviello89]

Hi. I'm also interested in this. Did you find a way to retrieve tissue expression in Zfin? thanks

Answer 1

[julien.roux]

We have integrated in situ hybridization data from ZFIN in the Bgee database (http://bgee.org/). You can download the expression calls as flat files, but please have a look at the BgeeDB Bioconductor package as well (http://bioconductor.org/packages/release/bioc/html/BgeeDB.html), since you can download these calls directly into R:

source("https://bioconductor.org/biocLite.R")
biocLite("BgeeDB")
library(BgeeDB)
myTopAnatData <- loadTopAnatData(species=7955, datatype="in_situ")
head(myTopAnatData$gene2anatomy)

Please note, that we also provide expression calls for many other animal species and from other data types (RNA-seq, Affymetrix microarrays and ESTs) Please do not hesitate to contact the Bgee team if you need more help: bgee -at- sib.swiss

[A. Domingues]

Cheers. I will test this (in a few weeks time), and report back.