Question: Convert Gene IDs of Tomato Sol Database
1
gravatar for kevluv93
4.3 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 • 5.4k views
ADD COMMENTlink modified 7 months ago by harrypotterandsbt50 • written 4.3 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 4.3 years ago by Lesley Sitter460

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 4.3 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 4.3 years ago by genomax73k

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

ADD REPLYlink written 4.3 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 4.3 years ago • written 4.3 years ago by genomax73k

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 2.1 years 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 3.6 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 2.2 years 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 23 months ago by petulkacat0

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 REPLYlink written 9 months ago by lqsdau0

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

Regards,

ADD REPLYlink written 7 months ago by alessandroriccini0

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 REPLYlink written 7 months ago by genomax73k

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

ADD REPLYlink written 7 months ago by alessandroriccini0
6
gravatar for kevluv93
4.3 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 4.3 years ago by kevluv93150

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

ADD REPLYlink written 4.2 years ago by A3.5k

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 3.6 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 2.6 years 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 2.3 years 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 2.3 years ago by genomax73k

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

ADD REPLYlink written 2.1 years 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 21 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 16 months ago by einatbrown0

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 REPLYlink written 10 months ago by salvatm180

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

ADD REPLYlink written 7 months ago by harrypotterandsbt50

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 REPLYlink written 7 months ago by sky0

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

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax73k

OK. Thanks for your reminding.

ADD REPLYlink written 7 months ago by sky0

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 REPLYlink modified 7 months ago • written 7 months ago by genomax73k

Got it. Thanks a lot.

ADD REPLYlink written 7 months ago by sky0
0
gravatar for Viswanathan
11 months 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 11 months ago by Viswanathan0

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

ADD REPLYlink written 7 months ago by harrypotterandsbt50
0
gravatar for alessandroriccini
7 months ago by
alessandroriccini0 wrote:

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 COMMENTlink modified 7 months ago • written 7 months ago by alessandroriccini0
0
gravatar for harrypotterandsbt
7 months ago by
harrypotterandsbt50 wrote:

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 COMMENTlink written 7 months ago by harrypotterandsbt50
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