Browse PSAMs

The main interface to the Yeast Transfactome consists of five different "tabs" that allow the user to view different kinds of data. We are first presented with the "Browse PSAMs" tab. Displayed here are all of the PSAMs for DNA-binding proteins that are contained in the database. One PSAM was derived for each available genome-wide occupancy experiment (e.g. ChIP-chip). Thus, we see a listing of affinity logos [3] for each experiment along with the name of the TF assayed and the citation for the source of the data that was used to create the PSAM. A button at the top of the page allows us to toggle between two different views of the PSAM list. The first view sorts all PSAMs by their goodness of fit to the original occupancy data. The t-value provides a guide for the highest quality PSAMs: the higher the t-value, the better the PSAM explained the original data. The other view sorts all PSAMs alphabetically by the common gene name of the TF. If we click on an affinity logo we can view the actual relative Kd values that constitute the PSAM and other details about the PSAM (example). We can click on any hypertext gene name to look up the TF in the Saccharomyces Genome Database [4].

Of the 399 DBP PSAMs in the Yeast Transfactome Database, 100 PSAMs corresponding to 52 DBPs are most similar to a PSSM from MacIsaac et al. [5] with the same factor identity. An additional 28 PSAMs corresponding to 11 DBPs are most similar to a PSSM from MacIsaac et al. [5] corresponding to a protein with which the analyzed factor is believed to have a physical or genetic association. Physical associations are significant in that an assayed factor may be bound to its target sequences indirectly via protein-protein interactions with a DBP. Genetic associations are significant as factors may have genetic interactions if they have the same sequence specificity (e.g. Msn2p and Msn4p). 59 PSAMs for 18 proteins are most similar to the TRANSFAC [6] matrix of the same protein identity, and 6 PSAMs for 4 proteins are most similar to a matrix for a protein with which the assayed factor has a physical or genetic interaction. Physical or genetic associations between factors were identified using BioGRID [7]. In the web interface, it is possible to view only those PSAMs that are consistent with one or both of the other sources of sequence specificities by checking the respective boxes and pushing the "Refresh" button.