Custom graphNEL object for pathview
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drowsygoat ▴ 20
@lechkaczmarczyk-14172
Last seen 15 months ago
Poland

Hi All,

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))] [1] "3' -UTR-mediated translational regulation" [2] "A tetrasaccharide linker sequence is required for GAG synthesis" [3] "A third proteolytic cleavage releases NICD" [4] "Abacavir transmembrane transport" [5] "Abacavir transport and metabolism" [6] "Abasic sugar-phosphate removal via the single-nucleotide replacement pathway" [7] "ABC transporters in lipid homeostasis" [8] "ABC-family proteins mediated transport" [9] "Acetylcholine binding and downstream events" [10] "Acetylcholine Neurotransmitter Release Cycle" > trans_path Reactome pathways for mmusculus 1 entries, retrieved on 24-04-2017 > trans_path <- trans_path[[1]] > head(nodes(trans_path)) [1] "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. I know there was a similar question asked here about 2 years ago, but I did not find the answer helpful.

Thanks in advance for any tips on that.

pathview mirintegrator miRNA • 705 views