Questions and Issues Dec, 2011

Go back to: Cosmoss-_Physcomitrella page

Also see Cosmoss, the Physcomitrella patens resource site.

Go to:Background info on Physco biology and culture

Excepted from email exchanges:

Reference page for the microarray data

It would be helpful to have a reference page or published reference to the microarray data cut-off points, based on established protocols.

SR: We are already working on converting all expression data that will go public via Genevestigator after the conference.

File format

Columns 1 instead of PP_Gene say COSMOSS

2 give us gene/locus id and not alias

   e.g. instead of Phypa_181133 give Pp1s47_77V2
   ONLY ONE ID PER ROW of ANNOTATION.

3 if you have assigned a gene symbol the give that if not repeat

   the value from column-2

4 leave it blank for now

5 this is fine as it stands

6 provide a publication id with this expression data.

   If not available type in a PMID of the genome
   paper as of now. Current value e.g. GB:PHYPADRAFT_181133 is not
   acceptable. Looks like GB:PHYPADRAFT_181133 is an
   alias(synonym).

7 this is fine as it stands

8 leave it blank for now

9 replace 'X' with 'S' if the PO id in column-5 is for anatomy.

    'G' if the PO id in column 5 is for growth stage.

10 gene name if you have any. If not leave it blank.

11 list all the aliases (synonyms) and deprecated IDs separated by

   the pipe (|) character. e.g. Phypa_181133|PHYPADRAFT_181133

12 replace 'transcript' by 'mRNA'

13 this is fine as it stands

14 this is fine as it stands

15 Is this expression data done by 'plantco.de' or 'COSMOSS'. If

   they are the same I suggest putting 'COSMOSS' otherwise it's
   fine.

We are working on getting the following two columns to be added to all the annotation files. Therefore, please take this opportunity to do so for Physcomitrella.

16 Leave it bank for now

17 provide the gene model id if you know one that's specific for

   expression (remember one model ID /lane). By default it is for
   the longest canonical/consensus gene model id. 

GO Annotations

DL sent a GOA file and it looks like the same format that we would need for the structure terms. I am not sure how to go about getting them submitted to the GO- Pankaj,