Is that brand new biosynthetic pathway or do you want to find homologues of known pathway? In what organism? Do you know how it goes (intermediates)?

Refer to Chapter 10. Neurospora, A Gateway to Biology, In FUNGI; Experimental Methods in Biology, CRC Taylor & Francis 2012. 

Dear tomas it is new pathway and only metabolites  involved in this biosynthetic pathway are predicted and we have any knowledge about genes involved in this pathway. it is sort of polyphenol biosynthesis pathway. this plant have medical use.

Dear Mohsen, it would be good if u could give a bit more data. What is your data? How many genes or metabolites do you have? GSEA tools such as david can predict you that which genes are enriched in which pathways? for metabolites there are other databases. If interested contact me ([email protected]).

dear Mohsen  I really agree with sadegh with use of DAVID or in other way if you only available with predicted sequences then better to perform homology analysis and predict functional domain of sequence and further analyse it under REACTOME or with KEGG pathway db and for plant especially you can go through plantgdb.org or pathway.gramene.org or plantcyc.org is good choice and ya if you be free to share data and more openly discuss problem then it would be more beneficial nd best of luck....... 

i searched all of internet to find information about this pathway but there was anything except a schematic pathway. i need a procedure to find what gene for what metabolite.

thanks all

Hi Mohsen,

Since you mentioned that "you have any knowledge of the genes" involved in the pathway (polyphenol biosynthesis), you can overexpress those genes to see how the polyphenol level changed in the transgenic plants, if your final goal is just to boost the production level of the 'polyphenol' (for example) in the particular medicinal plant you are working on. What do you think?

yes Yuan. i want to use elicitors to enhance metabolite production and then studying the mRNA profile by using of cDNA aflp and Creation of metabolite profile. after quantification of cDNA aflp bands by use of these data (two profiles) and integration of gene network to metabolite network, find what gene for what metabolites and vice versa. at this step we will be near to find what for what and more studies must be carried out to really find what gene for what metabolite. 

Thank you for your explanation, Mohsen.  Now, I know that your present goal is focusing on assign those 'predicted' genes onto this particular biosynthesis pathway through using some experimental data  (ex. profiles as you mentioned). And, I guess one day you may want to bioengineer this pathway by manipulating those genes for a specific metabolite production in this medicinal plant.

Thank Yuan. yes The ultimate goal of this study is engineering of that bio synthetic pathway. but we are still in initiate of this track