Convert Gene IDs of Tomato Sol Database

Question

[kevluv93]

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!

[Lesley Sitter]

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.

[kevluv93]

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

[GenoMax]

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

Which ID's do you have?

[kevluv93]

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

[GenoMax]

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

[bnkanyika]

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?

[mkoter]

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

[jamille_agronomia]

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 ([e-mail]). Thank you very much!

[petulkacat]

Please, could you also send to me the files with conversion of Solyc numbers to uniprot one? Thanks [e-mail]

[lqsdau]

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: [e-mail]. Thanks

[alessandroriccini]

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

Regards,

[GenoMax]

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.

[alessandroriccini]

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

[dimitrischat]

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

[aziz.hammou]

I am looking for this gene LOC101249187 ( NCBI Gene ID ) into the SolycXXgXXXXXX system

anyone can help ??

Answer 1

[kevluv93]

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.

[zizigolu]

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

[priya]

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!

[sibaez94]

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.

[gswang]

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 [e-mail]. And THANKS A LOOOOT!!!

[GenoMax]

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

[bnkanyika]

Hi. Would you still be able to share the file? My email is [e-mail]. Thank you.

[laracm]

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

[einatbrown]

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: [e-mail]

I would really appreciate it.

Einat

[salvatm18]

Hello Kevluv93, I'm also interested in this conversion. Would you send it to me, please? My personal email is [e-mail] Thanks a lot!

[harrypotterandsbt]

Hi. Kevluv93, Would you still be able to share the file? My email is [e-mail]. Thank you

[sky]

Hi Kevluv93 , I met the same issue recently. I would appreciate if you could send me the conversion sheet. My email is [e-mail]. Thank you.

[GenoMax]

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

[sky]

OK. Thanks for your reminding.

[GenoMax]

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.

[sky]

Got it. Thanks a lot.

[dimitrischat]

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

thanks in advance

Answer 2

[harrypotterandsbt]

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

Answer 3

[Viswanathan]

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"

[harrypotterandsbt]

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

[Viswanathan]

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.

Answer 4

[alessandroriccini]

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.