This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Group Genes by Protein Coding/Non-coding feature

Hi,

I have converted human ENSEMBL gene ids to GENE SYMBOL using AnnotationDbi package. So, I have a list of genes names like "TSPAN6","PDE11A". Is there any tool to group genes by protein coding and non-coding features? It could be a more detailed grouping also, but this broad grouping would also work for me.

Thanks in advance.

non-coding gene id_conversion coding
• 2,441 views • link
updated by GenoMax GenoMax • written by asumani asumani

Get Ensembl GTF file for human here. Uncompress using gunzip.

Protein coding genes:

$ grep protein_coding Homo_sapiens.GRCh38.104.chr.gtf | awk -F "\t" '{if ($3 == "gene") print $0}' | awk -F "gene_id |;" '{print $2,$4}' | head -10
"ENSG00000284662"  gene_name "OR4F16"
"ENSG00000186827"  gene_name "TNFRSF4"
"ENSG00000186891"  gene_name "TNFRSF18"
"ENSG00000160072"  gene_name "ATAD3B"
"ENSG00000041988"  gene_name "THAP3"
"ENSG00000142611"  gene_name "PRDM16"
"ENSG00000067606"  gene_name "PRKCZ"
"ENSG00000131584"  gene_name "ACAP3"
"ENSG00000169972"  gene_name "PUSL1"
"ENSG00000157911"  gene_name "PEX10"

You can look at gene_biotype field and create other groups.

• 0 views • link
written by GenoMax GenoMax

Thanks for the awk pipes! But I don't look for something like extracting information from GTF. I assumed there is already a tool which gives out the gene feature in gene_biotype given the gene symbol.

• 0 views • link
written by asumani asumani

You could use Ensembl BioMart to get that information then.

• 0 views • link
written by GenoMax GenoMax

please post example input, expected output and tried code (if there is any).

• 0 views • link
written by cpad0112 cpad0112

1 answer

extract only geneID and gene symbol from GTF file

For the above example, 4th column consists of gene_type (gene_class). You can use this information to group your list.

• 0 views • link
written by EagleEye EagleEye

Log in to answer this question.

More posts like this