What database would have a list of gene names and aliases for yeast?

Question

[dec986]

I'm looking for a database that would have a list of gene names, gene aliases, gene data, etc. for yeast. For example, the database should show that MDN1 and REA1 are the same gene.

I need to be able to download the database onto my laptop.

I've tried NCBI, yeastgenome.org, UCSC https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/database/ and old-fashioned googling but I don't see anything.

The "Download data" section on yeastgenome.org didn't yield anything.

thanks for your help

[Zhenyu Zhang]

I don't have much experience on the yeast side, but for human

• NCBI resource is the most reliable
• Ensemble resource is also trustworthy, but can miss some mappings
• UCSC resource has more wrong mappings due to the fact it is a transcript db instead of gene db. This might not be a big problem for yeast.

Answer 1

[GenoMax]

Using Entrezdirect: Gene names, description and aliases in that order.

$ esearch -db gene -query "Saccharomyces cerevisiae [ORGN]" | esummary | xtract -pattern DocumentSummary -element Name,Description, OtherAliases 
RAD52   recombinase RAD52       YML032C
SUP35   translation termination factor GTPase eRF3      YDR172W, GST1, PNM2, SAL3, SUF12, SUP2, SUP36
RAD51   recombinase RAD51       YER095W, MUT5

[dec986]

thanks, I'm checking that out now

Answer 2

[GenoMax]

Visit https://www.ncbi.nlm.nih.gov/datasets/gene/taxon/559292/

Click Select columns add/remove any columns you want. Be sure to select synonyms. Click "Apply". Select all genes using the check box in top left corner of the table. Then Download the Table.

Answer 3

[Wayne]

For powerful computational querying of such information for baker's yeast there is YeastMine:

"Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine."

There's a number of ways to get started seeking to build queries that you can then run and parse with your favorite software. For example, if you generate a query scheme, you can get the Python, Perl, Java, Ruby or other equivalents of the results and build those in to your pipeline as you see fit.

For example for your example, you can click on the 'Lists' option along the top banner and paste in MDN1 where it says 'Type/Paste in identifiers. It defaults to 'Gene' and so you can leave the other options (and more genes if you want) and press 'Create List' in the bottom left. Give it a name on the page that comes up and press the green 'Save a list ....' button on the right side. It will make a list with a 'default' set of columns with detail related to the gene or genes specified. You can add additional columns using the 'Manage Columns' button in the upper left. The window that comes up has a green button in the upper right you can press to 'Add a Column'. Near the top, you'll see additional items you can add like 'Sgd Alias' and 'Gene Summary'. Apply those changes and you'll see among the columns now 'Gene Systematic Name' , 'Gene Standard Name' and 'Gene Sgd Alias'. You can Export this table if you want and parse it subsequently. Or more importantly for scaling, you can choose a language to generate code that will recapitulate this process and data mining in your favorite language. The default is 'Generate Python Code' and you can use the drop-down adjacent to it to choose other options.

Alternatively for getting started building a query, there is the 'QueryBuilder' option listed along the top banner. This described as "Advanced users can use a flexible query interface to construct their own data mining queries." It may be helpful to click around and explore teh additional options there sometime.

Additionally, the predefined queries you can access under 'Templates' along the top banner give you a lot of examples that you can further customize with related forms. Try to find one close to the type of things you need to do and then click on it and see the form. At the bottom is an 'Edit Query' button that will open it in started form in 'QueryBuilder' tool. Or if the template happens to do much of what you want already you can actually click among the languages shown at the bottom (Perl | Python | Ruby | Java [help]) of template's main page and get the code in the language for doing that. You can then adapt it in the language of your choice.