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

Question

[harshraje19]

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

[ATpoint]

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.

[JC]

Ensembl Plant Biomart?

Answer 1

[Kevin Blighe]

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

[harshraje19]

This is working great. Thank you very much