Incomplete reactome.org all pathway level to ENSEMBL ID annotation files

Question

[kbaidzajevas1]

Hello,

I have got log2FC and FDR data from an RNA-seq experiment and I am picking values for specific pathway genes using reactome all level to ENSEMBL ID annotations in R. I downloaded the Ensembl2Reactome_All_Levels.txt file last October and only recently realised that there were some pathways missing, such as Glutamate and glutamine metabolism (R-HSA-8964539, created/last updated in the pathway browser on 10 Feb, 2017). I tried downloading the current version of the annotations and it did have the R-HSA-8964539 pathway, but there were also missing entries, such as ENSG00000282120 in Binding and Uptake of Ligands by Scavenger Receptors (R-HSA-2173782), which is annotated in last year's October annotations and the pathway browser. Has someone come across such a problem before and could help me solve it?

Thank you, Kajus

Answer 1

[darklings]

There is an R package (https://github.com/reactome/ReactomeContentService4R) which is the wrapper for the Reactome Content Service API.

Mapping an ESID (ENSG00000282120 in the question) to Reactome Pathway(s):

library(ReactomeContentService4R)
#> Connecting...welcome to Reactome v74!
pathways <- map2Events('ENSG00000282120', resource = 'ENSEMBL', species = 'human')
#> MapTo argument not specified, mapping to pathways... For reactions, specify mapTo='reactions'
nrow(pathways)
#> [1] 18
head(pathways, 3)
#>     dbId
#> 1 166663
#> 2 173623
#> 3 198933
#>                                                                displayName
#> 1                                         Initial triggering of complement
#> 2                        Classical antibody-mediated complement activation
#> 3 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
#>           stId    stIdVersion isInDisease isInferred
#> 1 R-HSA-166663 R-HSA-166663.2       FALSE      FALSE
#> 2 R-HSA-173623 R-HSA-173623.2       FALSE      FALSE
#> 3 R-HSA-198933 R-HSA-198933.6       FALSE      FALSE
#>                                                                       name
#> 1                                         Initial triggering of complement
#> 2                        Classical antibody-mediated complement activation
#> 3 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
#>   releaseDate  speciesName hasDiagram hasEHLD schemaClass className
#> 1  2006-08-02 Homo sapiens      FALSE   FALSE     Pathway   Pathway
#> 2  2006-08-02 Homo sapiens      FALSE   FALSE     Pathway   Pathway
#> 3  2007-08-21 Homo sapiens       TRUE   FALSE     Pathway   Pathway
#>                      doi
#> 1                   <NA>
#> 2                   <NA>
#> 3 10.3180/r-hsa-198933.2

Created on 2020-11-05 by the reprex package (v0.3.0)

As the message says, if you want to map the id to Reactions just specify the mapTo argument.

For many ids can do something like:

all.pathways <- lapply(ids, function(id) {
    map2Events(id, resource = 'ENSEMBL', species = 'human', mapTo = 'pathways')
  })