How to find the functions of Reactome pathways?
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3.2 years ago
Chaimaa ▴ 250

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

Pathways reactome pathways DAVID • 905 views
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3.2 years ago
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
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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!

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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.

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ok and then how to get its function?

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You can either go to ncbi biosystems or reactome website to search for the IDs. Or programmatically make a construct like:

https://reactome.org/content/query?q=ID1+ID2+ID3+ID4 for URL.

NCBI constuct (with eutils):

$ esearch -db biosystems -query "R-HSA-3371568" | efetch -db biosystems |  xtract -pattern System_names -element System_names_E
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3.2 years ago
Denise CS ★ 5.1k

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.

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6 weeks ago
darklings ▴ 280

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"

Created on 2021-06-14 by the [reprex package](https://reprex.tidyverse.org) (v2.0.0)

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