Question: how can i identify gene names from proteins ID?
0
gravatar for Learner
3.9 years ago by
Learner 220
Learner 220 wrote:

I have a list of proteins for example

A0A061ADQ1

O76618

A0A061AJ42

I want to find genes for each row . the proteins IDs are separated with a ;

any idea ?

genomics proteomics • 1.9k views
ADD COMMENTlink modified 3.9 years ago by Bioaln340 • written 3.9 years ago by Learner 220
0
gravatar for Jean-Karim Heriche
3.9 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

These look like UniProt accession numbers. If so, you can use UniProt's ID mapping service.

ADD COMMENTlink written 3.9 years ago by Jean-Karim Heriche22k

@Jean-Karim Heriche Yes they are coming from Uniprot

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Learner 220

Note: Those gene names appear to be Worm. Has IPA expanded beyond human, mouse and rat, the core genomes supported? Or were you hoping to map your work ID's into human and then use them?

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by genomax85k

@genomax2 to be honest , I don't know if it is possible to use Worm in IPA??? do you have any idea ? actually I used proteins ID and it only recognised 2000 out of 4000. it means half of proteins ID. what do you suggest ? how can I find out if IPA support Worm or not ? I think it works with worm too , look at this paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849582/

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Learner 220

Based on online help IPA supports ID' from C. elegans (14 total species but the core analysis only has Human/Mouse/Rat as main options). Looks like IPA can map only 50% of ID from your list so you need to investigate if that number can be increased. For efficient network identification IPA recommends that the # of genes be kept below 800. You are way over that limit.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by genomax85k

@genomax2 it means it support it , right ? also I used proteins ID and not gene names, do you think it make differences ? I saw that in 2013 people were converting non human gene list to human and then use IPA, do you have any idea whether this assumption still hold ?

ADD REPLYlink written 3.9 years ago by Learner 220

I don't know if "supports ID's from 14 species" does an internal mapping (to human genes, when needed) automatically. It may be best to confirm that with IPA tech support. Post here when you hear from them.

ADD REPLYlink written 3.9 years ago by genomax85k

@genomax2 It seems you are very good with IPA. I have one technical question. I have 6 samples 3 control which two of them are biological replicate and 3 bait which two of them again are biological replicate . Would you take the average of 3 control and then average of 3 bait and only import 2 values into the IPA or no, you will import all 6 ? or no, you will perform statistical test and calculate the fold change and import that one ?

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Learner 220

You probably either selected the wrong type of conversion or have a problem with your input. It worked for me just copy/pasting from your example above and selecting from Uniprot accession to gene name.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Jean-Karim Heriche22k
0
gravatar for natasha.sernova
3.9 years ago by
natasha.sernova3.7k
natasha.sernova3.7k wrote:

I took one of your IDs and searched for it in NCBI::

A0A061ACI3

www.ncbi.nlm.nih.gov

On the right panel for GENEs I’ve got:

One gene from Caenorhabditis elegans

http://www.ncbi.nlm.nih.gov/gene/?term=A0A061ACI3

And on the right panel fot PROTEINs I’ve got 2 proteins (the same) with different IDs for different databases(?):

http://www.ncbi.nlm.nih.gov/protein/?term=A0A061ACI3

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by natasha.sernova3.7k
0
gravatar for Bioaln
3.9 years ago by
Bioaln340
France
Bioaln340 wrote:

There are many options. If you are familiar with R you might want to look into

http://bioconductor.org/packages/release/bioc/html/UniProt.ws.html

If you like raw data approach, simply download the databases you want to work with and join them with e.g. bash or something similar. Getting genes from uniprot in the easier way is probbably using this: http://www.uniprot.org/uploadlists/

If not sure it will swallow all entries, split your files and do it in steps.

greets

ADD COMMENTlink written 3.9 years ago by Bioaln340

@Bioaln thanks, I have better solution by programming ! thanks anyway

ADD REPLYlink written 3.9 years ago by Learner 220
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