Question: Convert Gene IDs of Tomato Sol Database
1
gravatar for kevluv93
3.4 years ago by
kevluv93150
United States
kevluv93150 wrote:

I've ran a BLAST using the Sol genomics network database for my tomato transcriptome

http://solgenomics.net/

I have my transcriptome labeled with the sol gene IDs, but need to convert them to a more typical gene ID such as NCBI-geneID. Any thoughts on how to do this? I've tried using a series of different GeneID converters such as DAVID and biomart, but none of these programs have GeneIDs from the Sol Genomics network.

 

How do I convert these geneIDs? Thanks!

geneid convert gene • 4.2k views
ADD COMMENTlink modified 8 days ago by Viswanathan0 • written 3.4 years ago by kevluv93150

Do you know which Sol Genomics IDs correspond to which GeneID (like in a excell file or something)? Because if that is the case, then i can produce a simple script that does the translation.

If you are actually looking to query several databases than i'm sorry to say i can't help you.

ADD REPLYlink written 3.4 years ago by Lesley Sitter450

I can't find a chart with GeneID conversions. I'm combing the Sol Genomics website, but can't find it. I know that the tomato genome data is public and on several databases. If anyone has done this before or has the file please share the link. Right now typing in my keywords on google is yielding no results

ADD REPLYlink written 3.4 years ago by kevluv93150

There is this folder with ID conversion files: ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/id_conversion/

Which ID's do you have?

ADD REPLYlink written 3.4 years ago by genomax58k

Oh wow, there it is. I have the SolyC IDs that look like Solyc09g009710.2.1.

ADD REPLYlink written 3.4 years ago by kevluv93150

Unfortunately there does not seem to be any easy way (or a file) to easily translate those to NCBI ID's.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax58k

This is exactly what I am looking for. Amazing! Thank you. Is the link updated by the SOL genomics team or are the genes valid for the genome of 2 years ago?

ADD REPLYlink written 14 months ago by bnkanyika0

Hi, Could you please send me the tomato conversion sheet on my email: marek_koter (at) sggw.pl ? Thanks a lot, Marek D. Koter

ADD REPLYlink written 2.7 years ago by mkoter0

Hello, Kevluv93! I can not convert my Solyc to NCBI-gene ID. I would be grateful if you could send me the excel file to to my email (jamille_agronomia@yahoo.com.br). Thank you very much!

ADD REPLYlink written 15 months ago by jamille_agronomia0

Please, could you also send to me the files with conversion of Solyc numbers to uniprot one? Thanks petulkacat@gmail.com

ADD REPLYlink written 12 months ago by petulkacat0
6
gravatar for kevluv93
3.4 years ago by
kevluv93150
United States
kevluv93150 wrote:

Okay, so I finally completed this task by doing the following:

I contacted the Boyce Thompson Institute who ran the Sol Genomics website to see if they had any conversion sheets from their Sol genomics IDs to something more common. They sent me a very good conversion sheet of Sol gene IDs to UniProt IDs.

If someone knows how to share files on biostar I'll attach the conversion sheet to my answer. It's 1.7 MB, so not too big. I can't find the same file in the Sol genomics ftp directory, but I haven't looked that hard either. so if someone knows how to share files like this or if the file is on the sol genomics ftp directory, any help would be appreciated. 

So I got my sol gene IDs, got the sol to Uniprot IDs sheet, and used Galaxy to convert the sequences with the info on the conversion sheet.

Most gene enrichment analysis programs take the UniProt IDs, so this conversion did what I wanted it to do. 

Also this web based program can do Gene Enrichment analysis using the Sol gene IDs:

http://bioinfo.bti.cornell.edu/tool/MetGenMAP

Another good program that can use the Sol gene IDs for gene enrichment analysis:

http://mapman.gabipd.org/web/guest/home

So that's how I solved my issue. Thanks for the help guys.

ADD COMMENTlink written 3.4 years ago by kevluv93150

i installed mapman but it needs cdf file which i downloaded but mapman rejects that...

ADD REPLYlink written 3.3 years ago by F3.1k

Hi, I am facing the same issue. I need to do gene enrichment for tomato. I am trying to use MapMan, but would like to try using Enrichment Browser as well. Could you please email the conversion sheet to piya.venk(at)gmail ? Thanks a lot!

ADD REPLYlink written 2.7 years ago by priya0

Hello Kevluv93, I'm also interested in converting gene_IDs from Solyc code to NCBI. I would be really grateful if you could send me the excel file to my personal email sibaez94(at)gmail.com.

Tank you so much, Sergio.

ADD REPLYlink written 20 months ago by sibaez940

Hello Kevluv93, I'm also interested in converting gene_IDs from Solyc code to NCBI. I would be really grateful if you could send me the excel file to my personal email gswang@sibs.ac.cn. And THANKS A LOOOOT!!!

ADD REPLYlink written 16 months ago by gswang0

@Kevluv93 has not been seen on Biostars for a year and a half so you may want to figure out a plan B.

ADD REPLYlink written 16 months ago by genomax58k

Hi. Would you still be able to share the file? My email is bnkanyika@gmail.com. Thank you.

ADD REPLYlink written 14 months ago by bnkanyika0

Hello,

I'm currently doing RNAseq analysis on tomato and I'm facing the same issue, would you be able to share the file you mention to laracm at umich.edu?

I would really appreciate it.

Best, Cecilia

ADD REPLYlink written 9 months ago by laracm0

Hi,

I'm also currently facing the same challenge. Could you send me the conversion sheet of Sol gene IDs to UniProt IDs? my email: einatbrown@gmail.com

I would really appreciate it.

Einat

ADD REPLYlink written 5 months ago by einatbrown0
0
gravatar for Viswanathan
8 days ago by
Shanghai
Viswanathan0 wrote:

If you are using ITAG2.4, you can do the conversion here: http://www.uniprot.org/uploadlists/ In "2. Select options" choose "From: Ensembl Genomes Protein/Transcript"

In the output page: "Download" -> Format: "Mapping Table"

ADD COMMENTlink written 8 days ago by Viswanathan0
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