I have sequenced the transcriptome response of potato to pathogens using NGS (SOLiD ABI) and analyzed by clc bio Genomic work bench which determined the expression level (RPKM) compare to control and the function of genes also have been predicted using RNA-Seq of potato.
Now, I would like to input these sequences to MapMan software. Does anyone know how to input the sequnces to MapMan to be able to Map the genes with their expression level (upregulated and down regulated ). Thank you in advance.

Dear Rahim,

to be able to visualize your data you need an appropriate MapMan mapping file that assigns MapMan
functional categories (so called bins) to each of the sequence identifiers used in your data. We currently
have two mappings for potato that are publicly available - please check the mappings download site:

http://mapman.gabipd.org/web/guest/mapmanstore

If your reads have been mapped against one of these reference sequence sets (SGN unigenes or
PGSC) you can directly import your data files and use one of these mappings. If you mapped against a different
reference (e.g. your own transcriptome assembly) you'll have to generate a mapping using the sequeces
of your assembly first. This can be done automatically using the mercator pipeline:

http://mapman.gabipd.org/web/guest/app/mercator

I hope this answers your questions - if not don't hesitate to ask.

cheers,
Marc

Dear Marc,
I really appreciate it for your helpful answer. I should inform you that I am a new user of MapMan.
As a matter of fact, I have an Excel file of data which contains Feature ID and function based on the reference seq PGSC -DM-v3.4 and also the RPKM data. I tried to import the data in MapMan and use the PGSC data , but I was not able to show the expression leve (RPKM) and the information on the Map. please let me know whether I should use mercaptor pipline for my sequence data and after determining the BINs, import to the Map Man or I had problem with configuration of data in excel file.

About another set of my sequence data, I uploaded the sequences to the mercator pipline and tried to add the resulted data file to MapMan software. but, I got a message with the title : Error during data configuration: one data column should be selected at least ". As a matter of fact, I have only two columns, BIN code and Name, and selecting none of them can solve the problem. because I have got these data from SSH (subtractive suppression hybridization)

thank you in advance,
Rahim,

Dear Rahim,

there seems to ba a little misunderstanding - The files that Mercator produces are actually
the mapping files that contain the assignment of gene or protein identifiers to MapMan categories.
The data files that contains the actual numerical data (e.g. log fold changes etc) have to be provided
by you. We have published a detailed step-by-step guide to using MapMan that explains the
process and ideas behind it very well "The Ultimate MapMan Install and Usage Guide MapManGuid.pdf"
- this guide is available via the MapMan web site: http://mapman.gabipd.org/web/guest/mapman

Since you are new to MapMan I'd suggest you obtain a copy to get up to speed with the application.
If you have any further specific questions not answered in the guide don't hesitate to ask again.

cheers,
Marc

Dear Marc,
Thank you for your reply. I read the manual of software carefully and tried to upload my data step be step. After adding my data, I tried to visualize the data on a map. Based on the Pathway work flow, I selected the data set, Mapping of stub-PGSC-DM-v3.4 (because we have used it in our data asreference sequence ) and metabolism overview.
When I tried to visualize the patway, I got a message inwhich the data is not fit with the mapping. I found in the detail of the message that our data set identifier is like PGSC0003DMG400031495 whreas in mapping is like pgsc0003dmp400023743.
but when I use our data identifier in solgenomic network, I can find the function of gene easily.
Please let me know, how I can figure out this problem.

Thank you in advance,
Rahim,

Dear Rahim,

the problem seems to be that our mapping file was created based on the protein sequences,
and hence uses protein identifiers while your data uses the gene locus identifiers. Unfortunately,
these two don't match and that's why MapMan is issuing the error message.

I had a look at the example gene locus ID you sent in your post and found the following information
in the GFF3 annotation file that can be found on the FTP site of the sol genomics network
(PGSC_DM_v3.4_gene_nonredundant.gff)
... when searching the file for PGSC0003DMG400031495 you find the following GFF3 entry:

PGSC0003DMB000000451 BGI gene 194655 194969 . . . ID=PGSC0003DMG400031495;
PGSC0003DMB000000451 GLEAN mRNA 194655 194969 . - . ID=PGSC0003DMT400080875;Parent=PGSC0003DMG400031495;Source_id=PGSC0003DMG000040824;Class=2;
PGSC0003DMB000000451 GLEAN exon 194655 194969 . - . ID=PGSC0003DME400213395;Parent=PGSC0003DMT400080875;
PGSC0003DMB000000451 GLEAN CDS 194655 194969 . - 0 ID=PGSC0003DMC400054821;Parent=PGSC0003DMT400080875;

so there is a mRNA transcript annotated for this gene under the ID PGSC0003DMT400080875.
If i now use this mRNA ID to search the protein sequence file (PGSC_DM_v3.4_pep.fasta)
I find the following FASTA sequence :

>PGSC0003DMP400054821 PGSC0003DMT400080875
MIGRADIEGSKSNVAMNAWLPQASYPCGNFSDTSSFEFRRSKGSLGHAFT
VRIRTGNQNQTSFYPSVPHEISVLVELILGHLRYLVTDVPPQPNSPLDNV
FPPG*

meaning that the protein ID corresponding to the transcript that is expressed from the
gene locus PGSC0003DMG400031495 is PGSC0003DMP400054821.
So you would be able to use the protein ID based MapMan mapping file if you
translated all your IDs to the corresponding protein IDs using the above
described procedure....

which is obviously a hideously time-consuming and annoying task - i will have a look
at that and try to generate a gene locus-based mapping that i will then make available
via the MapManStore web page (so that you can download it directly from within
MapMan).

best greetings,
Marc

Hi again,

i have prepared a translation table (see attached) that you can use to find
the corresponding IDs.

I will create a mapping file based on this table

cheers,
Marc

Dear Marc,
Thank you for your attention and trying to solve my problem.
I tried to download the file Attachments: PGSC_DM_v3.4_ID_translation_table.txt (1,703.1k) , but it seems there is an error in the server and I could not download it.
Waiting for your good News,
Kind regards,
Rahim,

Hi Rahim,

it's an Excel file.... but for some obscure reason my mac version of excel has saved it with
a .txt extension. Please rename the extension to ".xls" and open it in Excel.

cheers,
Marc

Dear Marc,
I meant during downloading I get a message " Internal server error". Probably, your server has a temporary problem!.
Thank you,
Rahim,

Dear Marc,
I would like to know whether you could create a mapping file for PGSC DM v3.4 translation table.

kind regards,
Rahim,

Hi Rahim,

i just tried and from where i sit, the file downloads fine - so please retry. I guess the
problems you've experienced must have been of a temporary nature.

cheers,
Marc