June 10, 2015
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by Kachroo and colleagues. Another set was curated by Princeton Protein Orthology Database (P-POD) staff and is incorporated into SGD with their generous permission.
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.
You can access these data in two ways: using two new templates in YeastMine, our data warehouse; or via our Download page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!
YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we’ve created a series of short video tutorials explaining its features.
This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.
This template takes either human gene names (HGNC-approved symbols) or Entrez Gene IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We’ve created two new pre-made lists of human genes that can also be used with this template. The list “Human genes complementing or complemented by yeast genes” includes only human genes that are currently included in the functional complementation data, while the list “Human genes with yeast homologs” includes all human genes that have a yeast homolog as predicted by any of several methods.
If you’d prefer to have all the data in one file, simply visit our Curated Data download page and download the file “functional_complementation.tab”.