Convert Gene IDs of Tomato Sol Database
4
1
Entering edit mode
5.8 years ago
kevluv93 ▴ 160

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!

gene geneID convert • 7.0k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

Which ID's do you have?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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: qiangli@uga.edu. Thanks

ADD REPLY
0
Entering edit mode

I got an excel sheet with EntrezGENEid and EnsembleGENEid (Solyc). If you are interested in this file, let me know.

Regards,

ADD REPLY
0
Entering edit mode

You can post the file up on pastebin.com or as a gist on github.com. Then post the link in your answer from yesterday.

ADD REPLY
0
Entering edit mode

Sorry, but the file is too big for pastebin.com

ADD REPLY
0
Entering edit mode

hey, could you please send me this excel sheet? you need my email or something? thanks

ADD REPLY
7
Entering edit mode
5.8 years ago
kevluv93 ▴ 160

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 COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

Hello Kevluv93, I'm also interested in this conversion. Would you send it to me, please? My personal email is salvatm18@gmail.com Thanks a lot!

ADD REPLY
0
Entering edit mode

Hi. Kevluv93, Would you still be able to share the file? My email is 21707001sbt@zju.edu.cn. Thank you

ADD REPLY
0
Entering edit mode

Hi Kevluv93 , I met the same issue recently. I would appreciate if you could send me the conversion sheet. My email is l_ke0001@uni-muenster.de. Thank you.

ADD REPLY
0
Entering edit mode

Kevluv93 has not logged on biostars for 3 years. You will need to find an alternate way to get the information you need.

ADD REPLY
0
Entering edit mode

OK. Thanks for your reminding.

ADD REPLY
0
Entering edit mode

You should contact https://solgenomics.net/contact/form and see if you can get the file that Kevluv93 referred to. You may also want to suggest to them that this file be made available on their FTP site since many seem to need it off and on.

ADD REPLY
0
Entering edit mode

Got it. Thanks a lot.

ADD REPLY
0
Entering edit mode

could i have this id sheet please ? my email is dimitrischat @ gmail . com

thanks in advance

ADD REPLY
0
Entering edit mode
2.4 years ago

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 COMMENT
0
Entering edit mode

It can't work when I input a list of SolycXXgXXXXXX , and I cannot find the Download page

ADD REPLY
0
Entering edit mode

I am sorry for the delay. I cannot access certain sites properly from where I am. On Ensembl we now have genome build SL3.0. IDs should be in this form: Solyc01g005000.3.1. You can convert them to Uniprot IDs. Output

ADD REPLY
0
Entering edit mode
2.1 years ago

Hi, I found interesting this post because I looking for exactly the same. Just yesterday I found a sheet with the conversion of Solyc codes in Entrez gene ID (necessary for Mapman) You can find it at this link https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3786-3 Additional file 1. The problem is that a lot of Solyc are missing. If someone could improve this list and share I think it would be useful.

ADD COMMENT
0
Entering edit mode
2.1 years ago

Hello everyone,I think find an alternate. I suggest everyone use SL3.0 and corresponding gtf file to run RNA-seq workflow then we will get the result that most genes are labeled by LOCXXXXXXX。then we can use clusterProfiler(R package) : downloading tomato orgdb from AnnotationHub(),using bitr function from clusterProfiler to convert "SYMBOL" to "ENTREZID"。

Another solution is to download tomato annotation file from Ensemble Plant bioMart,you can download the whole file without any setting. If you know the Chiness ,you can read my post at https://www.jianshu.com/p/d9873cf6d073. But the problem is that maybe the data is out of date

ADD COMMENT

Login before adding your answer.

Traffic: 2499 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6