Question: Question on graphite/SPIA; extracting DE gene list
0
gravatar for rgamini
4.5 years ago by
rgamini0
United States
rgamini0 wrote:

Hi,

I am doing the SPIA analysis via **graphite package** for I could do the SPIA not just on KEGG pathway but on others such as reactome, nci etc.

So, one could use in graphite

prepareSPIA(db,"user_defined_string") (where, db can be KEGG, reactome, nci etc)
res <-runSPIA(de=my_DE, all=my_ALL, "user_defined_string")

head(res) ...

       Name                  pSize     NDE     pNDE            tA                    pPERT             pG                   pGFdr                      pGFWER  Status
1       Circadian rhythm        28      17      5.979811e-05    10.42313596     0.000005        6.856035e-09    1.028405e-06    1.028405e-06    Activated
2       ECM-receptor interaction        73      32      2.996008e-04    24.56547212     0.000005        3.193615e-08    2.395211e-06    4.790422e-06    Activated
-
Is there a way to extract the DE gene list using graphite/runSPIA ? For instance, how to list all the 17 (NDE) gene ids for circadian rhythm in the above example ?

Any suggestions/idea ? 

Thanks in advance.

Ramya Gamini

 

 

 

 

 

spia graphite runspia • 990 views
ADD COMMENTlink modified 7 months ago by Bioconductor Community ♦♦ 0 • written 4.5 years ago by rgamini0
1

Hi Ramya,

 

prepareSPIA creates a R data file, "keggexSPIA.RData", in the current working directory and the file contains a list with all the  pathways to be tested.

prepareSPIA(kegg, "keggex")

You can load that file:

load("keggexSPIA.RData")

and see the vignette of SPIA how to extract information from it. To get the Entrez IDs for instance you can use:

entids= sapplypath.info,"[","nodes")

names(entids)=gsub(".nodes","",names(entids))

# Entrez ids for the "Wnt signaling pathway"

entids[['Wnt signaling pathway']]

These ids may need to be intersected with the list of all genes on the array to get the hits per pathway used in the analysis.

Adi Tarca

ADD REPLYlink written 4.5 years ago by Tarca, Adi570
Answer: Question on graphite/SPIA; extracting DE gene list
0
gravatar for rgamini
4.5 years ago by
rgamini0
United States
rgamini0 wrote:

Works!!  Thanks much, Adi. 

Ramya

 

 

 

ADD COMMENTlink written 4.5 years ago by rgamini0
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