Software to reconstruct a proteomics-based metabolic pathway

Question

[anna]

Maybe this is not the appropriate web page for asking this but i don't know where to ask for help. Does anyone know if there's any software that can help me to reconstruct a proteomics-based metabolic pathway? In which I can load a data set containing the names of the genes and obtain a model or a graphical result (as an image)?

Answer 1

[Leite]

Dear anna

You can try ESCHER and MetaboAnalyst

Answer 2

[Mensur Dlakic]

KEGG should be a good starting point for you. You may need to upload a set of sequences instead of names.

Answer 3

[tbg]

I am a great fan of R and there are plenty of libraries to actually do bioinformatics. In this specific case I would recommend using the pathview library (see this link or this other link for some examples and help)

just to give you some working code that you may test, if you are familiar with R:

library("clusterProfiler")
library("pathview")
#this function provide you with some enrichment using kegg and entrezIDs for your genes
keggEnrich <- as.data.frame(enrichKEGG(entrezID, organism="mmu"))
#this function automatically exports some images with the metabolic paths
#it requires some parameters suche as the foldChange, kegg pathways name, the species you're referring to (in this case Mus musculus) and, finally, two parameters about colouring in the resulting image
pathview(gene.data=logFC, pathway.id=keggEnrich$ID[kegg], species="mmu", limit=list(gene=1, cpd=1))