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Presence of redundant IDS

Presence of redundant IDS
Answer
7/3/15 11:13 AM
Respected Sir/Madam

I am a Ph.D. student from NABI, Mohali India. I am working on de-novo transcriptome analysis of a fruit crop. I want to do pathway analysis using MAPMAN for my de-novo assembled transcriptome data. In that transcriptome data while doing assembly possible splice variant were predicted with different normalized FPKM values.
I don`t want to lose information of possible splice variant for pathway analysis. But since these are splice variant, they will be annotated with same IDs so that input files have redundant IDs with their FPKM values. And due to that MAPMAN is not accepting it.
As solution of that I had retrieved MAPMAN bin IDS corresponding to gene IDS, which also have redundancy.
Is it possible to use bin IDS with redundancy to plot pathway graphs?

I had gone through manual of MAPMAN, There is image annotate module. Can it be used to solve this problem?

Kindly suggest possible solution.
Early response will be highly appreciated.

With Regards

RE: Presence of redundant IDS
Answer
7/5/15 8:08 PM as a reply to Ashish Kumar Pathak.
Dear Ashish

we usually solve this by annotating all splice variants.
E.g. you have locus X1g000010 and two splice variants
X1g000010.1 and X1g000010.2 than you would maintain the .1 and .2 and annotate both. Be aware thought that this might mess up any pathway enrichment (e.g. in a pathological case you have one gene with 15 splice variants which you all call up-regulatedin this case for smaller pathways where the rest of the pathway has no splice variants you are likely to call this a pathway regulation but you need to be careful with the interpretation)

Best
Bjrön