enrichment to common gene
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Noy • 0
@7bb9ea1e
Last seen 24 months ago
Israel

Hello everyone, I compared 2 examples to find a list of common genes. Once I have found the common genes, I would like to find out the main processes to which these genes belong. I have an excel or CSV file with a table with a list of genes, the name of each gene and its GOs number. I do not have statistical information on each gene, how can I find the main processes/GO to which these genes belong? I would appreciate any advice. I have tried a number of free tools online (like David,categorizer etc.) but they do not come up with a short list of major GOs. I also tried with the "groupGO" but the problem is that in the "OrgDb" object the organism that I have worked with is none of the options so I dropped it from the code.

Just to clarify a few more things, the common genes are genes that in transcriptome analysis, have increased or decreased their expression levels and I compared the genes between two samples (each time only what went up / down) using the Venny tool so I have no statistical information about these genes, but only information that these genes are common. In addition to the list of genes I received, I found the name of the genes and the GOs of each one, the problem is that each gene has some GOs to which it is associated. I would appreciate any help/advice. Many thanks in advance! noy


# The elected genes 
down.comparison1<- read.csv("C:/Users/noy1/Desktop/RNASeq/down+LOC+GO.csv", header = TRUE, dec=".")

# reading in data from deseq2
df <-down.comparison1

# we want the log2 fold change 
#down.comparison1 <- df$log2FoldChange

# name the vector
names(down.comparison1) <- df$X

# omit any NA values 
gene_list<-na.omit(down.comparison1)

# sort the list in decreasing order (required for clusterProfiler)
gene_list = sort(gene_list, decreasing = TRUE)



groupGO( gene_list, keyType = "geneID2GO2.table", ont = "MF", level = 2, readable = FALSE )

#gse <- gseGO(geneList=gene_list, 
             ont ="ALL", 
             keyType = "ENSEMBL", 
             nPerm = 10000, 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             pAdjustMethod = "none")

Error in get_GO_data(OrgDb, ont, keyType) : 
argument "OrgDb" is missing, with no default
GeneSetEnrichment genes genetogo • 956 views
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