General Info

Blast Map

With each gene record there's a link to a graphic representation of that gene blasted against all other yeast genes with default blast parameters. The graphic is itself an imagemap with links to gene records of the blast hits.

Interactions

Genetic and Biochemical interactions are listed by default. This option can be turned off. The notation (L) means there's literature to support the interaction claim.

Expression Information

If gene expression profiles from certain fundamental experiments can be miniaturized such that they quickly convey the behavior of a gene then why not incorporate those empirical observtions into a database as a mini expression browser? The little expression graphics that appear are images made from the data sets of certain initial fundamental microarray experiments. I'll post references when i get a chance. Otherwise it should be pretty obvious what they are.

Linking to Records

To link to gene records from web pages you can construct a simple URL with the orf name as an argument. For instance:

http://www.phaget4.org/YGD/index.php3?orf=YGL043W

Thus a link constructed with that URL can bring up the database record for a given gene, such as YGL043W

Genelists

The Genelist link is a utility for returning gene information about a list of orfs or gene names. Sometimes papers just list a bunch of orfs, this can help to map information onto a list of names. It's also a good way to see how a list of your favorite genes behaved in several experiments at once. Sample Output

YGD can be curated by those who choose to use it. If you want to add something to a record there's a form for editing the database. Often when I'm sitting in a seminar I'll learn a whole bunch of things about a gene. One way to help me remember it is to enter the info into my database so it's there when I look up those gen es in the future. Why not have a community curated database? One way to learn about a lot of genes is to build a database about them and update it.

YGD was constructed with freely available tools such as linux, Perl, php and mySQL.

The things I'm looking to add are:

• Linking to other databases. When you want more information, or different information, or to see what the latest information is you should be able to get there with a mouseclick to SGD, MIPS, or YPD.
• Searchability on any field.
• Blast of yeast genes against other organisms and better synonym support.
• The ability to display information about groups of genes, i.e. all essential genes, all genes with introns, all genes involved in glycolysis, etc.
• I'd like to have some way of displaying visually (and in a very simple fashion) what pathway a gene is involved in. There must be some simple map-like description language, just like is used for displaying Yahoo! driving maps that could be used to sh ow a map of a gene's place in the cell.
• This may be related to the element directly above, but I'm thinking of incorporating information from geneontology.org.

Why haven't I added these things yet?

I don't have any time

Why YGD?

Often when I'm hunting around an array I don't need comprehensive information about a gene, I simply need concise information to remind me about what a gene does, or give me hints or clue s to a gene's function. So simple information is sufficient, and I can look up more details later with better resources.

I need access to yeast gene information regardless of what computer I'm on. Commercial databases are often free to .edu computers but if I'm at home I can't have access. YPD charges several tens of thousands of dollars per year for a license to it's database from a non .edu computer. I can't afford it.