how can i convert my gene list to a format that reactome recognises?

Question

[Learner]

I have a list of genes up-regulated.

But I don't know why the reactome does not recognise any of genes which are Uniprot. and I don't know to which format and how convert a big and large list of genes

Answer 1

[Denise CS]

The majority of those seem to be TrEMBL, unreviewed (computer annotated) entries from UniProtKB and could explain the absence of results from Reactome. O70209, Q91YJ3, Q91YJ5, Q8BM55 seem to be reviewed though. See more about those statuses here. It seems Reactome is human centric, so perhaps the above SW entries from mouse are still to be inferred from the human pathway counterparts? Human TrEMBL does not return any results in BioMart .e.g Q9NQR3 and Q15505. It may be a good idea to contact Reactome for a definitive answer.

[Learner]

@Denise - Ensemble Thanks ; do you know any way to search for a specific pathway when you have a list of genes? I am more interested in cancer pathway , I read few papers and google a lot but could not find a great web which allows me to target a specific pathway for my list

[Shamim Sarhadi]

If you have a ranked list of genes you could use GSEA pre-ranked desktop application and select a specific gene-set to enrich your gene list, simply you could use mysigdb http://software.broadinstitute.org/gsea/msigdb to search and enrich your gene list

[Learner]

@Shamim Sarhadi that is not a good way because of many reasons. One if the list a long then many error will appear.

[Shamim Sarhadi]

well, if your mean about error is the false discovery , I think after enrichment analysis with all tools that above mentioned you'll have values after multi test correction(FDR) and it limits the false discovery rate

Answer 2

[darklings]

Mapping non-Reactome ids to Reactome Events (Pathways or Reactions) when not considering any statistics:

library(ReactomeContentService4R)
#> Connecting...welcome to Reactome v77!

uniprot.id <- 'O95602'
pathways <- map2Events(uniprot.id, resource = "UniProt", species="human", mapTo = "pathways")

dim(pathways)
#> [1]  5 14
head(pathways, 1)
#>     dbId                               displayName         stId    stIdVersion
#> 1 427413 NoRC negatively regulates rRNA expression R-HSA-427413 R-HSA-427413.2
#>   isInDisease isInferred
#> 1       FALSE      FALSE
#>                                                                                                              name
#> 1 NoRC negatively regulates rRNA expression, Methylation of histones and DNA negatively regulates rRNA expression
#>   releaseDate  speciesName                    doi hasDiagram hasEHLD
#> 1  2014-03-12 Homo sapiens 10.3180/REACT_200856.1       TRUE   FALSE
#>   schemaClass className
#> 1     Pathway   Pathway

^{Created on 2021-07-23 by the [reprex package](https://reprex.tidyverse.org) (v2.0.0)}