bioMart biotype assignment
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5 days ago
imaparna27 • 0

Hello,

I am trying to assign bio-types to genes that I obtained after differential expression analysis. I used biomart for this purpose, but it retrieves only 54000 genes, whereas my expression data contains 57000 genes.

library(biomaRt)
ensembl = useEnsembl("ensembl",dataset="hsapiens_gene_ensembl", mirror = "useast")
genes <- df_RNA$gene_id
G_list <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id",
                                                          "entrezgene_id", "hgnc_symbol", "gene_biotype"), values=substr(genes, 1, 15), mart=ensembl)

What can be the possible error here, also what alternative to biomart can be used?

biomart • 372 views
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Did you use the same Ensembl version for both BioMart and to analyse differential expression?

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Yes, GRCh38.p13 for expression analysis as well as for bio-type assignment.

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The gene assembly has been 38.p13 since September 2019 but the gene annotation has been updated several times since then. What was the Ensembl version?

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version 17

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Version 17 was from about 2002

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Sorry about the previous details, I re-confirmed, I obtained FPKM data from TCGA database and they've used GENCODEv22 for alignment that I guess corresponds to GRCh38.p2. I used same versions for all annotations. But, I am not sure why still some of the genes being are yet unannotated in my results, however information for few them is present on the Ensembl website.

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You'll need to use Ensembl 80 to get GENCODE 22. Just include version=80 in your useEnsembl command.

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Thanks Emily_Ensembl, this really helped.

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Can you give some examples of the Gene IDs that are not being annotated?

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