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Is there any mapping of Oryza sativa leaf?

Is there any mapping of Oryza sativa leaf?
mapping database oryza sativa leaf rice
Answer
8/9/12 6:18 PM
Are there any other maps besides Oryza sativa roots likewise a mapping of the leaf in the database?

Best regards

Julian Kwoczek

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/10/12 11:14 AM as a reply to Julian Kwoczek.
Dear Julian,

i am not exactly sure if I understand what you are looking for - do you need a
graphical pathway representation of the rice leaf or a specific functional classification
(i.e. mapping) of rice leaf genes?

Best greetings,
Marc

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/12/12 10:38 AM as a reply to Marc Lohse.
Hi Marc,

I thought, that there is no need for a new graphical pathway, because these should apply for ervery plant species?! Therefore I just need a specific classicifaction of the rice leaf genes (a mapping of the rice leaf), but if the graphical pathway affects the mapping or the results in any way, i need both.

I hope I could express myself, because my English isn't quite well.

Best regards,
Julian

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/13/12 12:45 PM as a reply to Julian Kwoczek.
Hi Julian,

in principle, there is no need for a new pathway visualization, if you are satisfied with the ones that
are already available via the MapManStore (http://mapman.gabipd.org/web/guest/mapmanstore).

Likewise, there's also no need for a new rice mapping (i.e. assignment of gene/protein identifiers
to functional Bin categories) as long as the one also available via the MapManStore can be used
with your data. So, if the data you want to work with is e.g. chip data recorded on a rice
affymetrix array, you can start working with this directly (also, if the data is using TIGR5 or
MSU_v7 identifiers).

So - depending on what kind of data you have and how you want to visualize it - you might already
be ready to go.

Sorry for this quite unspecific answer, but i wasn't quite sure whether you had already tried
to use MapMan and couldn't because something was missing or whether your initial question
was just a general inquiry.

I hope this clarifies things for you a bit - if not, don't hesitate to post again!

cheers,
Marc

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 9:32 AM as a reply to Marc Lohse.
Hey Marc,

well, we were using Agilent.SingleColor.15241for the microarray. Is it still possible to evaluate the results with mapman because its a different platform compared to the ones you said?

Greetings Julian

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 10:44 AM as a reply to Julian Kwoczek.
Hi Julian,

i fear your data can not be used out-of-the-box. However, if the probe IDs used on your chip can be mapped to
the gene IDs for which a mapping exists, you can "translate" your data to the respoctive ID type and then use
it directly. Very often, AGILENT supplies a kind of cross mapping of the probe identifiers used on the chip to some
gene IDs - so please check your chip types supplementary data to find out if you already have this information.

If not, a gene to probe ID crossmapping can be made from scratch provided that the probe sequences are known.

Best greetings,
Marc

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 11:30 AM as a reply to Marc Lohse.
Okay. So i found out that my data has the Os numbers and the NCBI Acc. numbers. How can i write the Os number into MSU ID? Is there any program? If i do it by hand it will take years.. emoticon
For example: Os01g0532600|mRNA|AJ491820|CDS+3'UTR would be LOC_Os01g34850.1

Do you mean that by cross mapping?

Greetings Julian

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 12:18 PM as a reply to Julian Kwoczek.
Hi Julian,

i conducted a quick search and could not find anything that would allow batch translating the IDs you have
to the MSU v7 IDs. there are several tools and lists, however, that might help. Have you already tried this:

http://rice.plantbiology.msu.edu/analyses_search_converter.shtml

or mybe you can use this table:

ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/all.dir/rice.versions.info.txt.gz

If not, please tell me how you do the translation manually - maybe i can figure out a way to automate
this so that it becomes a doable thing (as opposed to translating 10 thousands of IDs manually...)

best greetings,
Marc

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 12:44 PM as a reply to Marc Lohse.
If you have old RAP IDs maybe this tool helps:
http://rapdb.dna.affrc.go.jp/tools/converter/run
(I don't know how many Ids can be converted though)

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 1:21 PM as a reply to Björn Usadel.
Ah perfect - thank you Björn, the download section of the page you linked
has exactly the table that is needed to translate the older Osxxxx IDs to
the MSU IDs. The full table is available here:

http://rapdb.dna.affrc.go.jp/download/archive/RAP-MSU.txt.gz

so, Julian, the problem is more or less solved. The only thing that
needs to be done is translating the IDs in your data file(s) to the
MSU IDs. This can be done in an automated way using a script -
i am happy to help you with this if you don't know how to do it.

cheers,
Marc

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 1:23 PM as a reply to Marc Lohse.
On second thought, it will probably be easier for everyone if I supply a mapping for the RAP
IDs using the translation table and make that available for download via the MapManStore.

Please allow 2-3 days for me to do this - when I am done i will post a message on this thread.

cheers,
Marc

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 3:04 PM as a reply to Marc Lohse.
This would be great! I hope it will work.

Thank you everyone.

Greetings Julian

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 4:46 PM as a reply to Julian Kwoczek.
The mapping is ready and can be downloaded via the MapManStore (http://mapman.gabipd.org/web/guest/mapmanstore)
or directly from within the MapMan application by clicking "Mappings"->"new Mapping"->"download" and the choosing
the Osa_RAPDB_mapping from the list.

The mapping was created based on the MSU v7 mapping and using the translation table provided at
http://rapdb.dna.affrc.go.jp/download/archive/RAP-MSU.txt.gz .

In total, 43076 of the MSU identifiers in the MSU v7 mapping could be associated with RAP IDs, while
23262 of the MSU IDs could not be mapped to RAP IDs.

If possible, we recommend users to use the MSU v7 mapping since the underlying genome release is
more up to date.

best greetings,
Marc

RE: Is there any mapping of Oryza sativa leaf?
Answer
8/22/12 5:54 PM as a reply to Marc Lohse.
Hi Marc,

I asked myself, if it is possible to write the RAP ID into the rice japonica mapping IDs? The MSU IDs are the same, but before every ID though stands osaj_nuc_
This mapping has more IDs compared with the MSU_v7 and therefore should be more useful.


Greetings Julian

RE: Is there any mapping of Oryza sativa leaf?
Answer
12/2/13 10:14 AM as a reply to Marc Lohse.
I don't suppose you've got a copy of that file? The site is down for maintenance!