Can anyone suggest me the tool to convert the gene ids to gene names?
1
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
gene
sequence
alignment
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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?