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how to add no display data

how to add no display data
答え
07/09/11 4:02
hi:
Six genes of WRKY changed in my chip data, but five genes changed in Mapman. How to add other one gene?Thank you

Re: how to add no display data
答え
07/09/11 8:48 Dear wlsxuへのコメント
Hi,

first question which array type and organism are you using?

Then best send me which one is missing (actual code),
as there are several reasons it is missing
-I might not have annotated is as a WRKY for many reasons (esp. for TFs finding sensible cutoffs is a tricky buissiness, so your input is more than welcome)
(you could search for the id and see if it is anywhere)
-It might not have translated over to the platform, e.g. when matching Affyids I reject multiple cross hybridizing ones as well as badly matching ones
-It could have been flagged as an obsolete gene by the upstream curators and removed
....

Generally when you think there is a lack/ missannotation please write me a line with the genecodes so it can get fixed in the next mapping file.
usadel AT mpimp-golm.mpg.de

Best Wishes,
Björn

Re: how to add no display data
答え
07/09/12 2:46 Dear wlsxuへのコメント
Hi,

Thank you for your letter

I use Affymetrix Arabidopsis ATH1. id,254231_at description,at4g23810 WRKY53 transcription factor activity. I searched ath_affy_tair6 of Mapman and didn't find it. How to add it?

Best Wishes,
Lei wang

Re: how to add no display data
答え
07/09/12 8:39 Dear wlsxuへのコメント
Hi Lei Wang,

ok this gene ended up in 35.3 (disagreeing hits) as of 2006-01-06 (TAIR:affy_ATH1_array_elements-2006-01-06) this was mapped to at4g23810 (WRKY) and at4g23800 (HMG), as these are different classes of TFs the corresponding Affy code was filtered out.

With TAIR7 gene models and the latest mapping (affy->agi) the affy code only hits your gene and is included again.
The TAIR7_affy mapping will be released with the newest MapMan version 2.1 due now.
(It offers more description and thus can't be used with an older MapMan version)

Best Wishes,
Björn

Re: how to add no display data
答え
07/09/12 10:08 Dear wlsxuへのコメント
Hi Björn,

Thank you for your early replay.

I use Version 2.0.0(23.09.2006)( http://gabi.rzpd.de/projects/MapMan/download/). Can you tell me where is the newest MapMan version 2.1?

I replace ath_affy_tair6 to Ath_AGI_TAIR7. Can I resolve this question.

Re: how to add no display data
答え
07/09/12 10:16 Dear wlsxuへのコメント
Hi,

sorry it will be uploaded during this week.

Björn

Re: how to add no display data
答え
07/09/12 13:37 Dear wlsxuへのコメント
wait MapMan version 2.1

Re: how to add no display data
答え
07/09/12 14:39 Dear wlsxuへのコメント
Hi,

How to use clustering visualization? help file is old.

Thank you

Re: how to add no display data
答え
07/09/13 12:00 Dear wlsxuへのコメント
Hi,

So you can use ath_affy_tair7 now with the latest version of MapMan (>=2.1.1).
Clustering is available by right-clicking on a dataset comprising several experiments.

In the help that should be covered by point 4.2 with a little graph.

Best Wishes,
Björn

Re: how to add no display data
答え
07/09/17 2:30 Dear wlsxuへのコメント
Hi,

I use ath_affy_tair7 now with the latest version of MapMan (>=2.1.1) and find 254231_at, But I use cell functions of Pathways and find DNA repair ID partially deleted(257669_at At3g20475 , 249016_at At5g44750). They change in my chip and are not export in Mapman. Are there partially deleted in others Pathways. How to solve it? ???


Best Wishes,
Lei wang

Re: how to add no display data
答え
07/09/17 8:55 Dear wlsxuへのコメント
Hi,

257669_at does not refer to any current Arabidopsis gene model anymore.

If you go to the TAIR microarray tool

http://www.arabidopsis.org/tools/bulk/microarray/index.jsp

you can check each probeset. 257669_at currently just results in "no_match".

Björn

Re: how to add no display data
答え
07/09/17 10:50 Dear wlsxuへのコメント
Hi Björn,

I am sorry, but in my chip it is described (id, 257669_at description, At3g20475 // 68416.t02314 DNA mismatch repair MutS family protein similar to SP|O43196 MutS protein homolog 5 {Homo sapiens}; contains Pfam profile PF00488: MutS domain V // tigr // 10 // ---). ID(249016_at) is described in my chip (At5g44750 // 68418.t05108 UMUC-like DNA repair family protein / BRCT domain-containing protein low similarity to Rev1S GI:12483635; contains Pfam profiles PF00817: ImpB/MucB/SamB family, PF00533: BRCA1 C Terminus (BRCT) domain // tigr // 10 // --- /// NM_123842 // Arabidopsis thaliana REV1 AT5G44750 (REV1) mRNA, complete cds. // refseq // 9 // ---).

I go to the TAIR microarray tool
http://www.arabidopsis.org/tools/bulk/microarray/index.jsp, and find id(249016_at) is here. how to explain it? Thank you.

Best Wishes,
Lei wang

Re: how to add no display data
答え
07/09/17 11:57 Dear wlsxuへのコメント
Hi,

is this the description from Affymetrix? Otherwise, there are different ways to map probesets to genes, but we stick to the TAIR one. We used to map by ourselves, but as TAIR uses a very similar procedure as ours, there is no reason to add to the confusion.

I would suggest that you stick with TAIR as well, unless you know exactly how the mapping (probesets to genes) was preformed.

Several groups used to use a both crude and imprecise way of mapping.

Björn