This is working great. Thank you very much
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harshraje19 •
Can anyone suggest me the tool to convert the gene ids to gene names?
After performing the Ht-seq count, i got following gene ids,
VIT_04s0023g03690 51 53 48 52
VIT_04s0023g03700 28 19 25 16
VIT_04s0023g03710 14 12 11 14
VIT_04s0023g03720 2 1 4 3
VIT_04s0023g03730 0 0 0 0
VIT_04s0023g03740 2 0 0 0
VIT_04s0023g03750 17 20 25 23
I want to convert these gene ids to gene names, can anyone suggest some software or command in linux for their conversion
Thank you
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Kevin Blighe
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harshraje19 •
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harshraje19 •
1 answer
The annotation for this species [Vitis vinifera; common grape] does not, indeed, seem great; however, there is information there via biomaRt:
library('biomaRt')
mart <- useMart(
biomart = 'plants_mart',
dataset = 'vvinifera_eg_gene',
host = 'plants.ensembl.org')
features <- getBM(
attributes = c('ensembl_gene_id',
'external_gene_name',
'external_gene_source',
'external_transcript_name',
'external_synonym',
'entrezgene_id',
'description',
'chromosome_name',
'start_position',
'end_position'),
mart = mart)
head(features, 12)
ensembl_gene_id external_gene_name external_gene_source
1 VIT_14s0108g01640
2 VIT_14s0108g01640
3 VIT_00s0246g00170
4 VIT_08s0056g00590
5 VIT_12s0028g01880 ROMT UniProtKB Gene Name
6 VIT_12s0028g01880 ROMT UniProtKB Gene Name
7 VIT_16s0100g01030
8 VIT_18s0076g00250
9 VIT_18s0001g15410
10 VIT_08s0007g07690
11 VIT_08s0007g07690
12 VIT_04s0044g00580
external_transcript_name external_synonym entrezgene_id
1 NDHB2 ndh2 4025030
2 NDHB2 ndh2 4025014
3 CCSA ycf5 4025038
4 CEMA ycf10 4025049
5 ROMT VvROMT 100233030
6 ROMT VvROMT 100217470
7 STS PSV368 100217471
8 SUC27 SUC27 100232846
9 GV-ADH1 GV-ADH1 100232853
10 PGIP PGIG 100232865
11 PGIP pgip 100232865
12 ACT1 act2 100232866
description
1
2
3 Cytochrome c biogenesis protein CcsA [Source:Projected from Arabidopsis thaliana (ATCG01040) UniProtKB/Swiss-Prot;Acc:P56770]
4
5 Trans-resveratrol di-O-methyltransferase [Source:UniProtKB/Swiss-Prot;Acc:B6VJS4]
6 Trans-resveratrol di-O-methyltransferase [Source:UniProtKB/Swiss-Prot;Acc:B6VJS4]
7 Stilbene synthase 3 [Source:UniProtKB/Swiss-Prot;Acc:P51071]
8 Putative sucrose transporter [Source:UniProtKB/TrEMBL;Acc:Q4JLW1]
9
10
11
12
chromosome_name start_position end_position
1 14 30191954 30192507
2 14 30191954 30192507
3 Un 17197906 17199144
4 8 884462 886252
5 12 2540839 2542441
6 12 2540839 2542441
7 16 16507726 16509479
8 18 15923548 15925964
9 18 13539135 13541625
10 8 21152228 21153570
11 8 21152228 21153570
12 4 21427866 21431057
Kevin
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I just had a look at the Ensembl annotation files for that species and it seems these kind of gene names are the only ones available. If you have a different source with more "intuitive" names feel free to post them (that would actually be the minimal effort you should invest) so we can have a look on how to convert your gene names.
Ensembl Plant Biomart?
As I said Emsembl does not seem to have any "human readable" gene names:
From that search, I only see one gene name in "Gene description" field in Ensembl BioMart.
Checking Phytozome data for Vitis v. seems the annotation for the species is bad.
My suggestion will be to try to annotate the list of genes using Blast2Go or similar tools.