Welcome to the MapMan Family of Software Forum

Please do not hesitate to register and post your question.

Don't forget to subscribe to your posted message so you get notified on updates.
Every question you post will help others and or enhance the software!

Post a question,   post a bug!

Welcome to the MapMen Family of Software Forum Welcome to the MapMen Family of Software Forum

Using MapMan

Mappings for FilteredGeneSet of B73 Maize

Hi,

I saw that you have mappings for the coding sequences of the Maize Filtered Gene Set. I have read count data from mapping Illumina paired end reads to the working gene set.
The expressions are like the example below.

Genes Cond1_1 Cond1_2 Cond2_1 Cond2_2
GRMZM2G374062 2579 1556 1905 1466
GRMZM2G374065 3161 1871 2315 1829
GRMZM2G374068 9 2 4 6
GRMZM2G374074 22 7 12 2
GRMZM2G374076 528 314 415 330

Map Man is not recognizing the gene ids when I tried the genome or the coding sequences maps as the mappings available with Mapman are that of transcripts. Do you have mappings for the Maize Working Gene or Filtered Gene Sets ? Is there any way we can get around this ?

Thanks in Advance,
Adarsh


Adarsh Jose
The Nikolau Group
NSF Engineering Center for Bio Renewable Chemicals
Iowa State University

RE: Mappings for FilteredGeneSet of B73 Maize
Answer
4/26/11 4:42 PM as a reply to adarsh jose.
Dear Adarsh,


I had a look in the file ZM_B73_5b_FGS_cds. and I have to say I am also no friend of multiple splice isoforms. The easiest is probably if you just added _t01 to your gene designations and looked what would happen. (you might loose a few transcripts)

Please also note, that MapMan is originally designed to visualize log2 fold changes. Now by going to multi experiment view you could still follow data with no reference. But as a global scaling strategy is used, you should probably log transform your data.

As Cond1_1 Cond1_2 Cond2_1 Cond2_2 seems to suggest some structure why not build expression estimates log2 fold changes etc, if this is possible.

björn