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If there is any data here that you wish to preserve, you are responsible for downloading it. An overview of the bioinformatics research being conducted at the Mathematics and Computer Science Division is available at this page. |
| Sentra Help Page Welcome to the Sentra database of prokaryotic signal transduction proteins. Our database has 2 main modules: our expertly annotated data sets (I) and those derived automatically (II). Sentra's main page (figure1) is the entry point to viewing or search these 2 modules.  Figure 1. Sentra's main page.
I. Viewing Expert Annotations Michael Galperin from NCBI has curated various class of signal transduction proteins in 202 prokaryotic organisms. Clicking on the the link for displaying these takes you to a list of all the organisms along with the number of signal transduction proteins he has identified (figure 2). CLicking on the number of proteins found for a particular organism will display the entire list of proteins he has identified along with links to the protein analysis page (figure 4).  Figure 2. Full list of expertly
curated organisms.
 Figure3. List of proteins identified by expert curation for Agrobacterium tumefaciens.  Figure 4. The protein analysis page. II. Automated Annotations We have identified two-component signal trasduction proteins based on domain composition (presence of signature domains) for complete and incomplete genomes. Our main search page allows for numerous way to search Sentra's automated results (figure 5). The first set of searches allows for searching against protein IDs (NCBI GI or UniProt accession), function keyword and InterPro accession(s). Multiple keywords and InterPro accessions can be entered and each entry is treated with the Boolean operator 'and'. No operators are allowed in the text boxes, only spaces. The results from this search are displayed and enable interactive analysis (see figure 6). The next set of searches shown in figure 5 is by signal transduction class (sensor, receiver, hybrid or all). Default selects against all organisms (complete or incomplete) or the user can select from the complete genome list. An intrim page is then displayed (figure 7) where the user can view all the results or filter that list by domain(s). Results from this page are agains displayed as shown in figure 6. You can also select an organism and view its pathway diagram (adapted from KEGG) and compare the pathway with those from other organisms (figures 8,9,10). The last way to search sentra is by phenotype. Selecting phenotype(s) will result in a list of organisms that meet the selected criteria. Organisms from this list can be chosen to search by signal transduction class.  Figure 5. Main search page in
Sentra
  Figure 7. After selecting organism(s) and class from the search page, you can view all the results or filter by domain composition.  Figure 8. Pathway analysis page. Shown is a pathway map for two-component pathways adapted from KEGG showing what was found in this particular organism. Selecting the genes to the left and clicking "analyze pwy" will allow the user to view the pathway with thos selected and make comparisions with other organisms.  Figure 9. Results from selected just the pho genes from E. coli K12. From here you can do pathway comparisons by clicking on the highlighted button. This will allow you select organisms to which one can compare.  Figure 10. After selecting organsims to which one wants to compare, the comparison table is displayed. If you have any further questions, please don't hesitate to contact us for further assistance (see Contact). |
