Hello guys, i have found some Reactome pathways from DAVID database and i want to know the functions of these pathways.
Can anyone help me to know their corresponding functions?
I appreciated any help!
Example;
R-HSA-3371568:R-HSA-3371568
R-HSA-445095:R-HSA-445095
R-HSA-3371571:R-HSA-3371571
R-HSA-3371453:R-HSA-3371453
R-HSA-3371511:R-HSA-3371511
https://www.ncbi.nlm.nih.gov/biosystems?term=((((R-HSA-3371568)%20OR%20R-HSA-445095)%20OR%20R-HSA-3371571)%20OR%20R-HSA-3371453)%20OR%20R-HSA-3371511
or
https://reactome.org/content/query?q=R-HSA-3371568+R-HSA-445095+R-HSA-3371571+R-HSA-3371453+R-HSA-3371511
We use the Reactome pathway information for our gene-disease associations in the Open Targets Platform. So you can use this URL to get information on R-HSA-3371568. Change the end of the URL for any other R-HSA ID you like for all the pathways in humans.
Fetching Reactome instances with standard IDs in R:
#BiocManager::install("ReactomeContentService4R")
library(ReactomeContentService4R)
#> Connecting...welcome to Reactome v76!
st.ids <- c("R-HSA-3371568", "R-HSA-445095")
instances <- lapply(st.ids, function(id) query(id))
str(instances, max.level = 2)
#> List of 2
#> $ :List of 23
#> ..$ dbId : int 3371568
#> ..$ displayName : chr "Attenuation phase"
#> ..$ stId : chr "R-HSA-3371568"
#> ..$ stIdVersion : chr "R-HSA-3371568.1"
#> ..$ created :List of 5
#> ..$ modified :List of 6
#> ..$ isInDisease : logi FALSE
#> ..$ isInferred : logi FALSE
#> ..$ name : chr "Attenuation phase"
#> ..$ releaseDate : chr "2014-03-12"
#> ..$ speciesName : chr "Homo sapiens"
#> ..$ authored :'data.frame': 1 obs. of 5 variables:
#> ..$ edited :'data.frame': 1 obs. of 5 variables:
#> ..$ literatureReference:'data.frame': 1 obs. of 11 variables:
#> ..$ orthologousEvent :'data.frame': 10 obs. of 15 variables:
#> ..$ reviewed :'data.frame': 1 obs. of 5 variables:
#> ..$ species :'data.frame': 1 obs. of 8 variables:
#> ..$ summation :'data.frame': 1 obs. of 6 variables:
#> ..$ hasDiagram : logi FALSE
#> ..$ hasEHLD : logi FALSE
#> ..$ hasEvent :'data.frame': 5 obs. of 15 variables:
#> ..$ schemaClass : chr "Pathway"
#> ..$ className : chr "Pathway"
#> $ :List of 23
#> ..$ dbId : int 445095
#> ..$ displayName : chr "Interaction between L1 and Ankyrins"
#> ..$ stId : chr "R-HSA-445095"
#> ..$ stIdVersion : chr "R-HSA-445095.1"
#> ..$ created :List of 5
#> ..$ modified :List of 6
#> ..$ isInDisease : logi FALSE
#> ..$ isInferred : logi FALSE
#> ..$ name : chr "Interaction between L1 and Ankyrins"
#> ..$ releaseDate : chr "2010-06-15"
#> ..$ speciesName : chr "Homo sapiens"
#> ..$ authored :'data.frame': 1 obs. of 5 variables:
#> ..$ edited : int 374671
#> ..$ literatureReference:'data.frame': 4 obs. of 11 variables:
#> ..$ orthologousEvent :'data.frame': 2 obs. of 15 variables:
#> ..$ reviewed :'data.frame': 1 obs. of 5 variables:
#> ..$ species :'data.frame': 1 obs. of 8 variables:
#> ..$ summation :'data.frame': 1 obs. of 5 variables:
#> ..$ hasDiagram : logi FALSE
#> ..$ hasEHLD : logi FALSE
#> ..$ hasEvent :'data.frame': 4 obs. of 14 variables:
#> ..$ schemaClass : chr "Pathway"
#> ..$ className : chr "Pathway"
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cpad0112 can you plz explain how you did that?
I want to do it one by one and if i want t know if these pathways have any relation to a specific disease how to check that plz?
Appreciated your help!
In OP data, pathway IDs duplicated and separated by :. Get rid of duplicate values and query NCBI biosystems or reactome. For eg in line "R-HSA-3371568:R-HSA-3371568" is duplicated and remove second or first one so that only one ID remains.
ok and then how to get its function?
You can either go to ncbi biosystems or reactome website to search for the IDs. Or programmatically make a construct like:
NCBI constuct (with eutils):