Getting all gene members in a Reactome Pathway
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3.1 years ago
The ▴ 170

I wish to get all genes present in a particular Reactome Pathway for H. sapiens. Ideally the input would be the names of the pathways or Reactome IDs (e.g.rRNA modification in the nucleus / R-HSA-6790901) and I would like to get back the genes present in that pathway.

Can any bioconductor package do that?

Thanks

Reactome Bioconductor • 2.7k views
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biomaRt package can do that, please read the manual here.

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16 months ago
darklings ▴ 480

Can use the Reactome Content Service wrapper in R: https://bioconductor.org/packages/devel/bioc/html/ReactomeContentService4R.html

Event to non-Reactome ids:

library(ReactomeContentService4R)
event2Ids(event.id = "R-HSA-6790901") # can only input id here
$geneSymbol
  [1] "WBSCR22"    "MERM1"      "HUSSY-03"   "PP3381"     "BUD23"      "TRMT112"    "AD-001"     "HSPC152"   
  [9] "HSPC170"    "DIMT1"      "DIMT1L"     "HUSSY-05"   "PNO1"       "NOP2"       "NOL1"       "NSUN1"     
 [17] "RNA45S5"    "28S rRNA"   "TSR3"       "C16orf42"   "UND313L"    "FBL"        "FIB1"       "FLRN"      
 [25] "NOP58"      "NOL5"       "NOP5"       "HSPC120"    "SNU13"      "NHP2L1"     "NOP56"      "NOL5A"     
 [33] "NAT10"      "ALP"        "KIAA1709"   "THUMPD1"    "NOC4L"      "NOL11"      "L14"        "UTP18"     
 [41] "WDR50"      "CDABP0061"  "CGI-48"     "WDR3"       "UTP6"       "C17orf40"   "HCA66"      "MHAT"      
 [49] "WDR36"      "TBL3"       "SAZD"       "PWP2"       "PWP2H"      "FCF1"       "C14orf111"  "CGI-35"    
 [57] "DCAF13"     "WDSOF1"     "HSPC064"    "KRR1"       "HRB2"       "WDR46"      "BING4"      "C6orf11"   
 [65] "FP221"      "DHX37"      "DDX37"      "KIAA1517"   "RPS14"      "PRO2640"    "DDX47"      "RPS6"      
 [73] "OK/SW-cl.2" "EMG1"       "C2F"        "DDX49"      "UTP14C"     "KIAA0266"   "UTP14A"     "SDCCAG16"  
 [81] "RPS9"       "RPS2"       "RPS4"       "SNORD3A"    "RRP9"       "RNU3IP2"    "U355K"      "RCL1"      
 [89] "RNAC"       "RPC2"       "RPCL1"      "RTC2"       "HSPC338"    "BMS1"       "BMS1L"      "KIAA0187"  
 [97] "PDCD11"     "KIAA0185"   "NOP14"      "C4orf9"     "NOL14"      "RES4-25"    "RRP7A"      "CGI-96"    
[105] "NOL6"       "RRP36"      "C6orf153"   "HSPC253"    "RPS7"       "UTP11"      "UTP11L"     "CGI-94"    
[113] "HDCMB12P"   "MPHOSPH10"  "MPP10"      "IMP4"       "BXDC4"      "IMP3"       "C15orf12"   "MRPS4"     
[121] "UTP3"       "CRLZ1"      "SAS10"      "DDX52"      "ROK1"       "HUSSY-19"   "UTP4"       "CIRH1A"    
[129] "cPERP-E"    "KIAA1988"   "UTP15"      "HEATR1"     "BAP28"      "UTP10"      "WDR43"      "KIAA0007"  
[137] "UTP5"       "WDR75"      "UTP17"      "DIEXF"      "C1orf107"   "DEF"        "UTP20"      "DRIM"      
[145] "NHP2"       "NOLA2"      "HSPC286"    "GAR1"       "NOLA1"      "DKC1"       "NOLA4"      "NOP10"     
[153] "NOLA3"

...
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3.1 years ago
alserg ▴ 770

There is a package reactome.db: http://bioconductor.org/packages/release/data/annotation/html/reactome.db.html There you can select genes from reactome pathways. However, the IDs are not consistent with the online version, although pathway names are consistent.

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