[Drosophila] FlyAtlas.org: Major upgrade and 7 new tissues added

Julian Dow via dros%40net.bio.net (by j.a.t.dow from bio.gla.ac.uk)
Wed May 20 18:02:17 EST 2009


http://flyatlas.org is an Affymetrix microarray-based atlas of gene 
expression in multiple tissues of adult and larval Drosophila 
melanogaster. It been accessed by over 12000 users in the last 
sixmonths, from nearly everywhere except Alaska.

We are delighted to announce the addition of 7 new tissues!
  Adult eye,
  adult fat body,
  adult heart,
  larval CNS,
  larval trachea,
  larval carcass,
  S2 cells (growth phase).

We have also updated our local copies of allied data (Biogrid, 
Homophila, NetAffx etc) that are linked from FlyAtlas, and harmonised 
what gets displayed for each gene across the different searches.

Data quality
We take great pride in the purity of the dissections, as evidenced by 
high enrichments relative to whole fly. Here are some interesting 
selections you can check out on the database:

  Adult eye:
Of course, there will be some bleed-through to the head samples, but 
novel gene CG13840, Ecdysone-inducible gene L1 and shaker cognate B are 
all pretty specific.

  adult fat body:
There's not much of this to be found in 7-day adults, so we see some 
cross-talk with other tissues. You should use this data cautiously. 
However, Turandot X (immunity) and and insulin receptor suggest that the 
data are OK.

  adult heart:
This is Venkat's trickiest dissection to date, and so perhaps it's not 
surprising to see a bit of cross-talk with fatbody. But neuromancer1 
(H15), muscle-specific-homeodomain-2 (tin) and Bteb2 ( a homologue of a 
gene associated with Waardenburg syndrome) are good examples of specific 
genes.

  larval CNS:
Warniu, doublesex-Mab related 99B and tailless are UTTERLY larval 
CNS-specific (i.e. not in adult CNS either).

  larval trachea:
This is a pretty clean sample (though you might also expect some 
bleed-through to adult or larval carcass). However, there are some 
highly specific, under-researched genes, like CG34199, CG6696 and 
CG13047, all at least 10x enriched. And ecdysis triggering hormone-2 
(ETH) - WOW!

  S2 cells (growth phase):
With an organism with such potent genetic tools, I confess to being 
under-excited by cell lines. But there are some low-level transcripts we 
haven't seen anywhere else, like Gustatory receptor 94a or the novel 
transcript HDC08464.

---

Overall, then, these new tissues are useful both to illuminate the 
tissues in question, and to add authority to the tissue specificity of 
genes expressed elsewhere.

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For scriptwriters, programmatic calls to the database are possible, e.g.
http://flyatlas.org/atlas.cgi?name=CG1147
You can search with FBgn, CG number, Affy oligo, gene symbol or free text.

These data were prepared and placed in the public domain as a service to 
the Drosophila community, by the UK’s Biotechnology and Biological 
Sciences Research Council (BBSRC) through their Investigating Gene 
Function (IGF) and bioinformatics and biological resources (BBR) 
initiatives. Over the last 4 years, our facility has provided 1000 free 
Affymetrix arrays to the UK fly community. Further details at: 
http://www.mblab.gla.ac.uk/igf/

Enjoy!
     Julian Dow (j.a.t.dow from bio.gla.ac.uk)





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