SGD Help: Function Junction
Contents
The Function Junction allows users to simultaneously search a variety of functional analysis project sites for all available functional information for a given gene or ORF.
- Selecting a Set of Functional Analysis Sites to Search:
There are currently six different functional analysis sites that can be searched
using Function Junction. Function Junction can search one, several,
or all of the databases at a time in any combination. In order to
choose the sites you would like to search, click the gray
buttons next to the names of the desired sites. By default,
all six sites are searched.
- Entering a Gene Name:
One gene or ORF
name may be searched by Function Junction at a time. Type the gene or
ORF name into the box at the bottom of the form labelled "Enter a gene
or ORF name." The wildcard
character (*) can be added at the end and/or beginning of the gene
or ORF name. For example, to retrieve all the sterile genes, enter
"ste*".
After typing in the name to be searched, click the box "Submit" to
begin the search.
- Description of the Sites and How They Are Queried:
The different sites that can currently be searched in
Function Junction are listed below. Included is a brief description
of each site and how it is queried by Function Junction.
- SGD SAGE Query (Johns Hopkins and Stanford University)
- Description: This study described in Velculescu, et al., (1997) Cell 88:243-251 examined gene expression on a genomic scale using the SAGE technique.
- Query by SGD SAGE: Function Junction queries the SAGE data stored at SGD for gene names associated with a SAGE tag and returns a table with any SAGE tag(s) associated with that gene along with the expression data for the tag(s) as well as positional information.
- Yeast PathCalling (CuraGen & University of Washington)
- Description: The Yeast PathCalling project is a collaboration between Stan Fields lab at the University of Washington and CuraGen Corporation to identify proteins that are likely to form complexes with other proteins. This work is described in Uetz et al., (2000) Nature 403:623-7.
- Query by Yeast PathCalling: The Function Junction
searches the Yeast PathCalling site for the gene name entered and retrieves a brief description of the gene as well as a both a text list and graphical display of potential interacting proteins.
- YGAC Triples Database (Yale University)
- Description: This project utilizes transposons to
analyze phenotypes, localization, and expression of yeast genes on a
genomic scale. There is a link to a list of relevant publications on the Triples home page.
- Query by YGAC Triples Database:The Function Junction
searches the YGAC Triples Database for the entered gene name and retrieves the Triples results page. From the results page, you can click on the highlighted clone ID to get phenotypic, localization, and expression information for the given clone.
- Worm-Yeast Protein Comparison (Stanford University)
- Description: This study compared all of the predicted proteins from C.elegans and S. cerevisiae. This analysis is described in detail in Chervitz et al., (1998) Science 282:2022-2028.
- Query by Worm-Yeast Protein Comparison: The Function Junction searches the Worm-Yeast Comparison data and retrieves the BLAST report and a list of shared similarity groups in which the given gene is present.
- Yeast Protein Function Assignment (UCLA)
- Description: The Yeast Protein Function Assignment project assigns functions to yeast proteins using methods described in Pellegrini et al., (1999) Proc. Natl. Acad. Sci 96:4285-4288 and Marcotte et al., (1999) Science 285:751-753
- Query by Yeast Protein Function Assignment: Function Junction searches the Yeast Protein Function Assignment page by ORF name and retrieves a list of ORFs to which the given ORF name is functionally linked.
Function Junction can be accessed by selecting "Search SGD" from the menu bar at the top of most SGD WWW pages, then clicking on the "Function Junction" link below.
Global Gene Hunter: tool at SGD that simultaneously searches multiple databases including Genbank, YPD, MIPS, and others.
Expression Connection: search the results of several microarray studies for gene expression data for a given gene or ORF.
Go to Function Junction
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