Dear friends,
I need the steps in insilico pathway reconstruction. please suggest me best tools in this area. and i had the info about Genes, Proteins, Compounds for flavonoids pathyway of solanaceae plants... With this info is it possible to consttruct a partial pathway. Im new to this.. please help me... its urgent... Thank you...
Hi..make a list of all the genes and proteins together... and use "SubPathwayMiner" package of R, this will do the pathway enrichment analysis...thereby you identify all the pathways which are affected/regulated by ur gene list.
this might give you some insight into how ur genes are involved in...
Apart from that, you can download the gene interaction data from ppi databases like strings, DIP etc...find out the interacting partners for ur gene list..then use the above mentioned R package so that you can hav a broader range of claasification of ur genes...or use cytoscape for the interacting partners that u identified from ppi databases and make ur own network....
i hope u understood little bit of this n might be helpful to u...
thank you sir... after that how to refining the pathway?? how to check is it rite??
hi...yeah this is bit tedious job...
there are so many ways...first either go for literature search try to find out the experimental evidences for those interaction... secondly do the transcription factor profiling this will give u the key nodes i.e. hub genes...then u can go for some wet lab experiments n validate those interactions...
thank you sir.... My research topic is "Computational genomics of evoluion and reconstruction of anthocyanin pathway in solanaceae"... i finished the evolution part... now my guide is out of station.... i have to finish the in silico pathway recinstruction with in 20 days... this is insilico... i had the genes, proteins and compounds identify by literature review and homology searching... there is any way to finish this part with the collected info??? I depend the research gate only for my methods... i dont know how to initiate... very new to this...
do you have micro-array data for this??
and what kind of data you have from literature search? like genes involved in anthocyanin pathway or is it some interaction data?
do you have micro-array data for this??
and what kind of data you have from literature search? like genes involved in anthocyanin pathway or is it some interaction data?
Dear sir, Thank u lot...
i got interaction data from KEGG, PLANTcyc, METAcyc... From literature i got componends which is the final products of the pathway and responsible for pigment express.... and also genes... by using petunia plant genes which coding for enzymes catalyzing and regulating the anthocyanin pathway i found the homologs in CHIllI and EGGPLANT and many solanaceae plants... i have to construct pathway for chili and eggplant..
i dont have microarray data...
see if you have interaction data then u can directly make a interaction network through cytoscape.... or do 1 thing try to find out the interaction(either gene or protein) data for Solanaceae....
if u come up with the interaction datasets then we can identify interaction set for ur set of genes...first find out interaction data set....
ok sir..... with all the info i catch u soon..... i hope u will help...
thank u...
sir, my mail id: [email protected].... 2mrw or day after tomorrow i will contact u with all gene components reactions info... please tell the steps... then i will proceed.... thank u...
Dear sir,
I had 40 flavonol derivative compounds... for that 2 reactions only identified in arabidopsis..... in main path i had all the compounds , proteins, genes and reactions...in which format i have to prepare the data?? in xl sheet??
path: phenylpropanoid path--->flavonoid path: flavonols, flavones, anthocyanins and their derivatives
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