I would like to compare miRNA and mRNA sequencing results using
Pathview. By default,
Pathview uses a KEGG xml file downloaded using the function
pathview(). My first problem is how to feed
Pathview with a custom pathway (for example a reactome pathway converted into graphNEL object)?
I am using
mirIntegrator package, to integrate miRNA interactions into KEGG pathways. mirIntegrator package contains a function keggPathwayGraphs(), which downloads KEGG pathways. Then, these pathways are augmented by integrating miRNA interactions into gene networks. The resulting pathways (augmented pathways) are graphNEL objects, looking as follows:
> augmented_pathways_mmu_04727 $`path:mmu04727` A graphNEL graph with directed edges Number of Nodes = 218 Number of Edges = 748
I could not figure out how to input a graphNEL object made of reactome pathway. This is what I was trying:
> library(graphite) > MouseReactome <- pathways("mmusculus", "reactome") > names(MouseReactome)[1:10] > trans_path <- MouseReactome[grep("transmission",names(MouseReactome))]  "3' -UTR-mediated translational regulation"  "A tetrasaccharide linker sequence is required for GAG synthesis"  "A third proteolytic cleavage releases NICD"  "Abacavir transmembrane transport"  "Abacavir transport and metabolism"  "Abasic sugar-phosphate removal via the single-nucleotide replacement pathway"  "ABC transporters in lipid homeostasis"  "ABC-family proteins mediated transport"  "Acetylcholine binding and downstream events"  "Acetylcholine Neurotransmitter Release Cycle" > trans_path Reactome pathways for mmusculus 1 entries, retrieved on 24-04-2017 > trans_path <- trans_path[] > head(nodes(trans_path))  "A0A087WR33" "A0A0A6YW90" "A0A0G2JEA7" "A0A0G2JFW0" "A0A0N4SWF8" "A0A0R4J239" > head(edges(trans_path)) src dest direction type 1 A0A087WR33 A0A0G2JFW0 undirected Binding 2 A0A087WR33 A0A140T8S1 undirected Binding 3 A0A087WR33 D3Z685 directed Control(Out: ACTIVATION of BiochemicalReaction) 4 A0A087WR33 D3Z685 undirected Binding 5 A0A087WR33 D3Z6K8 directed Control(Out: ACTIVATION of BiochemicalReaction) 6 A0A087WR33 D3Z6K8 undirected > trans_path "Neurotransmitter receptors and postsynaptic signal transmission" pathway Native ID = R-MMU-112314 Database = Reactome Species = mmusculus Type of identifiers = UNIPROT Number of nodes = 175 Number of edges = 1600 Retrieved on = 24-04-2017 # creating a GRAPHnel object of the pathway; these gives an error with mirIntegrator > trans_path_g <- pathwayGraph(trans_path) > trans_path_g A graphNEL graph with directed edges Number of Nodes = 175 Number of Edges = 2068 > augmented_pathway <- integrate_mir(trans_path_g, mirTarBase) Error in as.list.default(X) : no method for coercing this S4 class to a vector
On the other hand, with a graphNEL object generated using
keggPathwayGraphs() everything seems to be working fine:
> kegg_pathways_mmu_04727 $`path:mmu04727` A graphNEL graph with directed edges Number of Nodes = 88 Number of Edges = 542 > augmented_pathways_mmu_04727 <- integrate_mir(kegg_pathways_mmu_04727, mirTarBase) > augmented_pathways_mmu_04727 $`path:mmu04727` A graphNEL graph with directed edges Number of Nodes = 218 Number of Edges = 748
The second problem is how to use such a custom (augmented) pathway (graphNEL) for visualization using Pathview. What I would like to achieve is a Pathview-rendered visualisation (KEGG or Graphviz) including color-coded fold changes of both, mRNAs (genes) and miRNAs.
Any tips on how this can be achieved I will very, very much appreciate.
Best wishes, Lech