[Genome] fly phenotypes

[Ann Zweig]

Hello Sean,

	There is a way to get the phenotypes using a join in the Table Browser. 
  Use the Table Browser to join the flyBaseGene table to the fbPhenotype 
table. There is a small catch -- the flyBaseGene table uses transcript 
IDs which are CG*-RA, -RB etc.  This should work fine if you make a 
modified list of your identifiers, with wild-cards, separated by spaces 
not newlines, e.g.

CG11686-R? CG18170-R? CG10799-R?

and paste that into the name box on the filter page (that should work
even for several hundred IDs), and then do a selected fields query.

The tables are related in the following manner:

fbPhenotype.geneId -> flyBase2004Xref -> flyBaseGene.name


Step by step:

1. Choose the dm2 flyBaseGene table from the Table Browser.
2. Press the 'filter' button and enter your modified identifier list 
into the name field.  Press the 'submit' button to return to the main 
Table Browser page.
3. Choose as output format "selected fields from primary and related 
tables".
4. Press "get output"
5. From this 'join' page, you will join the flyBaseGene table to the 
fbPhenotype table (using the intermediary flyBase2004Xref table).
   5.a. Check the name field of the flyBaseGene table.
   5.b. Choose the flyBase2004Xref table, then press the "Allow 
Selection From Checked Tables" button.
   5.c. Choose the fbPhenotype table, then press the "Allow Selection 
 From Checked Tables" button.  Check all four fields in this table.
   5.d. Press the "get output" button.


	If there is a phenotype available, it will be described in the 
fbPhenotype.text field:

#filter: (flyBaseGene.name like 'CG11686-R_' OR flyBaseGene.name like 
'CG18170-R_' OR flyBaseGene.name like 'CG10799-R_')
#dm2.flyBaseGene.name	dm2.fbPhenotype.geneId	dm2.fbPhenotype.fbAllele 
dm2.fbPhenotype.fbRef	dm2.fbPhenotype.text
CG11686-RA	FBgn0040551,FBgn0040551,	17524,17524,	118,4225,	Phenotypic 
class: viable Phenotypic class: fertile,Phenotypic class: viable 
Phenotypic class: fertile,

	Be sure to let us know if these instructions are not clear.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Sean Bradley wrote:
> Hi Gurus. I feel like I should be able to get fly phenotypes for a
> list of identifiers from the table browser, but that doesnt appear to
> work. There isnt always a phenotype Im sure, but if there is I would
> like it for a few hundred genes like these:
> CG11686
> CG18170
> CG10799
> Thanks and keep up the great work!
> Sean
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