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I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp

I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below:

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I want to convert the .gmt file into a dataframe. And it should look like below:

enter image description here

can anyone say how I can do that. Thanq

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  • $\begingroup$ This might be an XY problem (you are asking about a problem, but you really have another one). Why do you need this data in data.frame format? Also consider that the GO data is a directed acyclic graph, which has a special structure that should be taken into account $\endgroup$
    – llrs
    Commented Nov 8, 2018 at 12:25
  • $\begingroup$ for some analysis I want the data to be looked like the output I posted. $\endgroup$
    – beginner
    Commented Nov 8, 2018 at 13:17
  • $\begingroup$ Also note that the GO annotations imported by MSigDB are quite old. If you are interested in associations between GO and genes (updated) you should use other sources $\endgroup$
    – llrs
    Commented Nov 8, 2018 at 14:28
  • $\begingroup$ other resources like? $\endgroup$
    – beginner
    Commented Nov 8, 2018 at 14:47
  • $\begingroup$ Like the GO database directly or PANTHER. Or to retrieve the results biomart or its package biomaRt $\endgroup$
    – llrs
    Commented Nov 8, 2018 at 15:41

3 Answers 3

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Ok. Answering my own question.

I did this way. And I got the output I want.

install.packages("msigdbr")
library(msigdbr)

m_df = msigdbr(species = "Homo sapiens", category = "C5")
head(m_df)

Output:

gs_name gs_id gs_cat gs_subcat human_gene_symb~ species_name entrez_gene
  <chr>   <chr> <chr>  <chr>     <chr>            <chr>              <int>
1 GO_14_~ M184~ C5     MF        AANAT            Homo sapiens          15
2 GO_14_~ M184~ C5     MF        AKT1             Homo sapiens         207
3 GO_14_~ M184~ C5     MF        ARRB2            Homo sapiens         409
4 GO_14_~ M184~ C5     MF        BAD              Homo sapiens         572
5 GO_14_~ M184~ C5     MF        DAB2IP           Homo sapiens      153090
6 GO_14_~ M184~ C5     MF        DDIT4            Homo sapiens       54541
# ... with 2 more variables: gene_symbol <chr>, sources <chr>

found this solution from here https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html

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  • $\begingroup$ perfect! thanks. $\endgroup$
    – Ahdee
    Commented Dec 18, 2019 at 18:19
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You can import the csv file as a table. This does not require further libraries:

#you're reading a csv file, using tab as field separator and considering the first line as the headers of the data table
data <- read.csv(filename, sep="\t", header=TRUE)

then what you need are just two columns of your data:

colnames(data) #will give you the names of the columns that can be accessed
#to access two columns and merge them into a selectedColumns table
selectedColumns <- cbind(data$colName1, data$colName2)
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  • $\begingroup$ The question is tagged with R so it is an R data.frame. $\endgroup$
    – llrs
    Commented Nov 8, 2018 at 12:21
  • $\begingroup$ you're right! I missed it $\endgroup$
    – gbt
    Commented Nov 8, 2018 at 12:51
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You can use GSA.read.gmt function from GSA package. The following code can be used to convert the file to a dataframe. Just ignore the warnings.

Original_response

library(GSA)
data <-  GSA.read.gmt("c5.all.v6.2.symbols.gmt")
gene_names <- unlist(data$genesets, use.names=FALSE)
your_dataframe <- cbind(data$geneset.names,gene_names)
colnames(your_dataframe) <- c("Pathways","Genes")
mydataframe <- as.data.frame(your_dataframe)
head(mydataframe)
                                               Pathway   Gene
1            GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION POLR2C
2                           GO_CARDIAC_CHAMBER_DEVELOPMENT POLR2J
3 GO_DNA_DEPENDENT_DNA_REPLICATION_MAINTENANCE_OF_FIDELITY  CTDP1
4                                      GO_CIRCADIAN_RHYTHM   RDBP
5              GO_PHOSPHATIDYLSERINE_ACYL_CHAIN_REMODELING COBRA1
6                               GO_SPINAL_CORD_DEVELOPMENT   RSF1

Edited_response

You can use the code given below to achieve your desired output:

library(GSA)
data <-  GSA.read.gmt("c5.all.v6.2.symbols.gmt")
len_vec=c()           # Now create a vector for containing the length of genes at each position
len_vec[1] = 3
for(i in 1:length(data$genesets)){len_vec[i] <- c(length(data$genesets[[i]]))}
pathway_vec <- unlist(Vectorize(rep.int)(data$geneset.names, len_vec),use.names = FALSE) # Now create a vector for all the pathways in the data 
desired_df <- as.data.frame(cbind(pathway_vec,unlist(data$genesets,use.names = FALSE))) # This gives your desired dataframe
head(desired_df)
                                    Pathway      Gene
1 GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION POLR2C
2 GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION POLR2J
3 GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION  CTDP1
4 GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION   RDBP
5 GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION COBRA1
6 GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION   RSF1
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  • $\begingroup$ sorry, this is wrong. Please check the output I want in the above question. In your output Genes POLR2J, CTDP1, RDBP, COBRA1, RSF1 shows different pathways. $\endgroup$
    – beginner
    Commented Nov 8, 2018 at 13:02

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