Blog:list of old gene name in C. elegans

Question

[firoz.imtech]

Hi,

Gene of C. elegans may have two different names. For instance, WBGene00006993 has two locus name: (1) "zyg-8" and, (2) old/other names "apo-1" (http://www.wormbase.org/species/c_elegans/gene/WBGene00006993#0-9e-3). I have compiled (1)WB id, (2)locus, and (3)cosmid id of all genes from C. elegans GFF3 annotation file (Version WS240). However, I also need other names associated with WormBase id as I described in the example. I am not getting this information from GFF3 file. Could anyone kindly tell me the best way to get all the "other names" information.

Thanks a lot,
Firoz

Answer 1

[geneontologyhelp]

Did you try WormMine or AllianceMine? The InterMine data warehouses have all the info you've compiled/need, including all IDs used by WormBase.

Using the AllianceMine List analysis:

https://www.alliancegenome.org/alliancemine/bag.do

• Select Type: Gene
• for Organism: C. elegans
• I recommend uploading longer lists of identifiers (.txt).

Use the "Create a list" button, and after doing any needed disambiguation use the green "Save a list of n Genes".

On the following "List Analysis for gene list you just loaded" page, use Manage Columns (upper left) -> Green "Add a Column". Find "Synonyms" in this list, about 2/3 down the list. Click it and select Value. You'll see the green "Add 1 new column" button in top right, click that then Apply Changes.

Export using the top right button.

Note, this process should be nearly the same for any of the organisms in the Alliance (fly, mouse, rat, budding yeast, worm, xenopus, zebrafish).