Enrichpathway In ReactomePA.

When I am trying to do enrichpathway in ReactomePA package, I am getting zero observation. No entrezid is mapped.

> gene<-c("64240", "6296", "196883", "153", "155", "4299", "2334", "79026", 
    "9495", "1109", "23294", "50636", "343", "394", "50649", "23204", 
      "728619", "440", "23300", "90135", "695", "399947", "84645", 
     "401027", "401097", "727", "767", "57685", "23473", "858", "126075", 
        "6348", "6351", "901", "729230", "952", "1013", "54825", "10715", 
         "79094", "337876", "163732", "51192", "22866", "256076", "594855", 
         "1373", "1395", "122011", "8048", "8530", "441521", "115908", 
         "1511", "340578", "8526", "729582", "1742", "58512", "28514", 
         "1756", "26052", "1791", "100130771", "93556", "8672", "954", 
         "2034", "83715", "83648", "400823", "2274", "23768", "114984", 
        "118924", "9846", "2650", "219970", "653641", "2974", "51454", 
        "3040", "54435", "55363", "3091", "9454", "59340", "51214", "3554", 
        "3653", "122953", "386679", "54900", "116842", "3963", "3981", 
         "22998", "114038", "158038", "80350", "84918", "10150", "79150", 
         "440823", "4312", "4352", "56667", "83955", "79923", "89796", 
         "606", "9611", "64067", "4883", "56675", "9378", "4914", "126014", 
         "165140", "10039", "23037", "221692", "51588", "118788", "10769", 
         "51090", "23129", "5435", "285755", "5504", "29968", "11168", 
         "5733", "5746", "22931", "378948", "51308", "5979", "57127", 
         "56163", "649946", "6278", "6286", "148418", "6403", "710", "5274", 
         "26040", "81537", "83699", "148641", "85414", "159963", "6536", 
         "23657", "55512", "6619", "100126781", "84973", "26770", "728524", 
        "6689", "6696", "6704", "6708", "6767", "90627", "6779", "474338", 
         "100130958", "85360", "1155", "122402", "7006", "100124696", 
         "7015", "7019", "53346", "284186", "160418", "8794", "7293", 
         "7170", "7173", "373", "7222", "1831", "7291", "7302", "10537", 
         "10720", "80329", "7402", "7422", "79674", "7453", "9589", "54739")

>> yy = enrichPathway(gene, pvalueCutoff=0.05)

>>head(yy)

[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue      geneID     
[9] Count      
<0 rows> (or 0-length row.names)

r reactomepa

• 2,711 views • link

updated 8.3 years ago by Ram

• written 8.3 years ago by bikash2510 •

Have you followed the [vignette][1] properly?

There is the hypergeometric model building for total number of genes and readable=T parameter

library(ReactomePA)
data(geneList)
de <- names(geneList)[abs(geneList) > 1.5]
head(de)
x <- enrichPathway(gene=de,pvalueCutoff=0.05, readable=T)
head(as.data.frame(x))

Check your command lines once again.

• 0 views • link

written 8.3 years ago by ivivek_ngs

Please provide feedback on your previous posts. You have multiple people waiting for your input. The posts will be marked inactive in 48 hours if there is no response from you.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

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written 8.3 years ago by Ram

Hello bikash2510!

We believe that this post does not fit the main topic of this site.

See C: Enrichpathway In ReactomePA.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written 8.3 years ago by Ram

1 answer

> yy
#
# over-representation test
#
#...@organism    human
#...@ontology    Reactome
#...@keytype     ENTREZID
#...@gene    chr [1:198] "64240" "6296" "196883" "153" "155" "4299" "2334" "79026" ...
#...pvalues adjusted by 'BH' with cutoff <1
#...441 enriched terms found
'data.frame':   441 obs. of  9 variables:
 $ ID         : chr  "R-HSA-1234158" "R-HSA-6783783" "R-HSA-6794361" "R-HSA-6785807" ...
 $ Description: chr  "Regulation of gene expression by Hypoxia-inducible Factor" "Interleukin-10 signaling" "Neurexins and neuroligins" "Interleukin-4 and 13 signaling" ...
 $ GeneRatio  : chr  "3/111" "4/111" "4/111" "5/111" ...
 $ BgRatio    : chr  "11/10513" "49/10513" "57/10513" "108/10513" ...
 $ pvalue     : num  0.000178 0.00173 0.003024 0.005646 0.006349 ...
 $ p.adjust   : num  0.0784 0.3815 0.4446 0.5197 0.5197 ...
 $ qvalue     : num  0.0773 0.3761 0.4382 0.5123 0.5123 ...
 $ geneID     : chr  "2034/3091/7422" "6348/6351/729230/3554" "1742/58512/9454/9378" "3091/4312/79923/7291/7422" ...
 $ Count      : int  3 4 4 5 3 2 2 3 2 4 ...
#...Citation
  Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for
  reactome pathway analysis and visualization. Molecular BioSystems
  2016, 12(2):477-479

No pathway passed your criteria, i.e. p.adjust < 0.05.

• 0 views • link

written 8.3 years ago by Guangchuang Yu

But I am not getting the result as you mentioned here. Please, could you tell me how to do that? And I have to reduce my P-value to 0.01 to get significant pathways.

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written 8.3 years ago by bikash2510 •