BioCyc Guided Tour

This page provides a tour of some of the information pages available through the EcoCyc/BioCyc website.

A convenient way to take the guided tour is to keep this page visible in one tab in your Web browser, while viewing the other pages listed in a separate browser tab.

Use Case: Find Genome Information

1. Begin the tour at:
   • EcoCyc gene/protein page for tyrB / tyrosine aminotransferase
   • Click on the different tabs about four inches down the page, such as "Protein Features"
   • Click on the "Operons" tab

2. In the resulting operon diagram, click on the "Show Details" button to display:
   • Transcription-unit page for Transcription unit tyrB

3. On the "Site 1" line, click on "TyrR-Tyrosine DNA-binding transcriptional repressor" to display:
   • Transcription-factor page for TyrR-tyrosine repressor

4. Back in the gene page for tyrB
   • Click on the "View in Genome Browser" button to view: Genome browser focused on tyrB
     • Hover the mouse over a gene for more information
     • Use the zoom controls in the upper left to zoom in/out or move left/right

5. Back in the gene page for tyrB, click on the "Align in Multi-Genome Browser" in the right-sidebar menu on the far right. Select a set of organisms in the next page and click Submit near the bottom of the page. The resulting page will align the tyrB gene across all the selected organisms, when present. Example:
   • Comparative genome browser focused on tyrB

Use Case: Find Pathway and Metabolite Information

1. Enter the words "leucine biosynthesis" in the search field near the top of most pages, then click on the pathway name "L-leucine biosynthesis" in the search-result page to see:
   • Pathway page for L-leucine Biosynthesis

2. Within that pathway display click on the arrow for the last reaction to display
   • Reaction page for EC 2.6.1.42

3. Click on the chemical structure of leucine in the reaction page to display
   • Compound page for leucine
   • Click on several of the tabs, such as "Regulation", to see additional information
   • Click on the "Reactions" tab and scroll to the bottom of the page

Use Case: Navigate Metabolic and Regulatory Networks

• From the Tools menu at the top of the page, click on "Metabolism → Cellular Overview" to display the Cellular Overview (metabolic map diagram) for E. coli. This diagram can be magnified using the ladder on the left, or by scrolling with the mouse wheel. Mouse over an element of the diagram to identify it. Search for enzymes or metabolites using the right-sidebar menu, example, such as: "Highlight Compound(s) → By Name or Frame ID", then enter L-tryptophan.
  • For a guide to painting transcriptomics or metabolomics data onto the diagram, see sample data files and animations.

• Click on "Tools → Genome → Regulatory Overview" to display a regulatory network diagram for E. coli. A pop-up legend describes the diagram's gene symbols and concentric rings. This diagram can also be magnified, and mousing over gene symbols identifies them.

Use Case: Search Other Organism Databases

• Let's now look at information for another organism, Faecalibacterium prausnitzii A2-165. You can make it the current organism that BioCyc searches as follows:
  • Click on the blue "Change Current Database" button towards the top of the page
  • Enter the strain name "A2-165" into the entry box underneath the phrase "Select a Database"; then click the full organism name that appeared; then click OK
  • The resulting page provides statistics on the content of the database and the data source from which it was generated

  • Next, to find information about this organism enter one of these phrases in the search box towards the top of the page. Click on a result from the search results page and review the information available.
    • dehydroquinate biosynthesis
    • L-arginine
    • ssB

Use Case: Comparative Analysis