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 ?
These look like UniProt accession numbers. If so, you can use UniProt's ID mapping service.
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(?):
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
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version 2.3.6
@Jean-Karim Heriche Yes they are coming from Uniprot
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?
@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/
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.
@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 ?
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.
@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 ?
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.