Enrichement with clusterProfiler and biomartr

Question

[sansan96]

Hello,

I am trying to perform functional enrichment with clusterProfiler and BioMart but I am having the following error:

**Starting BioMart query ...
Error in biomaRt::getBM(attributes = as.character(c(filters, attributes)), :
   Invalid attribute(s): SYMBOL, SYMBOL
Please use the function 'listAttributes' to get valid attribute names**

I understand that it is for SYMBOL, but I don't know which one is correct.

My identifiers are like this: Zm00001eb002010

Could you help me?

My code:

# Set working directory
setwd("C:/todos/Diferenciales_lgn")
list.files()

# Read the DESeq2 table
diff_genes <- read_delim(file = "UP_lgn_vs_WT_filtrado_estricto.csv", delim = ",")

# Assign names to the first column
colnames(diff_genes)[1] <- "genes"

# Create a new table with the columns of interest
diff_genes <- diff_genes[, c("genes", "log2FoldChange")]

# Save the new table to a file
write.table(diff_genes, file = "diff_genes_up_maiz.tsv", sep = "\t", row.names = FALSE, quote = FALSE)

# We retrieved the zmays_eg_gene dataset from genome annotation version of the plant_mart mart.
biomartr::organismBM(organism = "zea mays")

#We retrieve attributes from zmays_eg_gene for Zea mays
zea_attributes <- biomartr::organismAttributes("zea mays") %>% 
  filter(dataset == "zmays_eg_gene")

# We obtain the correspondence between the Zea mays gene identifier and the NCBI Entrez gene identifier.
attributes_to_retrieve <- c("SYMBOL", "entrezgene_id")

result_BM <- biomartr::biomart(
  genes = diff_genes$genes,
  mart = "plants_mart",
  dataset = "zmays_eg_gene",
  attributes = attributes_to_retrieve,
  filters = "SYMBOL"
)

head(result_BM)
listAttributes (mart, zmays)

[Ram]

You're using biomartr, not biomart. Please correct your question title and tag

[jv]

cross-posted: https://support.bioconductor.org/p/9156018/#9156021

Answer 1

[jv]

As pointed out in the answer you received on Bioconductor, there is no attribute called SYMBOL that you can retrieve.

Have you looked at MaizeDB? There is a tool "Translate Gene Model IDs - download" on https://www.maizegdb.org/gene_center/gene where you can paste your list of Zm... identifiers (up to 8000 at a time). There are a few options for what to convert your identifier to, but if you are planning to use clusterProfiler you'll want to select "GeneBank Gene Accessions (Entrez)" to get entrez gene ids.