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About Arabidopsis G-Signaling Interactome Database:

This database includes information on Arabidopsis proteins identified to interact with the heterotrimeric G-protein complex. Three proteins (RGS, GPA1, and ARD1) and two dimers (AGB1/AGG1 and AGB1/AGG2) were chosen as the first set of baits (core baits). After the preliminary screening, 22 proteins were chosen as the second set of baits. Using a high-throughput interaction screening with 22 baits against 9 cDNA libraries, a total of 396 prey proteins with 903 interactions were identified. See below for information about the cDNA libraries used. See the project website for more details on the data collection experiments.

Information on these baits, preys, interactions, and libraries are stored in our G-signaling MySQL database. The graphic user interface allows users to search through our database and gather information of interests using Web browsers. Protein information for baits and preys is gathered from TAIR (The Arabidopsis Information Resource) and stored also locally in our database. Interactions are visualized using N-Browse.


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Site Information:

  • Home
    • Shows the current statistics of bait, prey, and interaction data in our database. Each number is linked to a specific page. Or use the tabs at the top of the page to navigate through the website.
  • Baits
    • Lists bait proteins used for the interaction analysis. The bait table serves as a portal for information about preys and interactions.
      • Show Interaction Summary by Bait button brings up the Interaction Summary page. See below for the description for this page.
      • Bait Locus is linked to its entry in TAIR database for more information.
      • The button in the Interaction column shows the number of interactions for each bait. See the description below Bait Specific Interaction Summary page.
      • Interactions from the bait can be visualized using N-Browse by clicking on either TAIR or N icon button. A preview of the network image can be seen by rolling over the icons. TAIR icon launches N-Browse Java Applet from TAIR with TAIR interactome database. N icon launches N-Browse Java Applet from our server with our G-signaling interactome database.
      • AtPID link brings up the Bait locus information from AtPID (Arabidopsis thaliana Protein Interactome Databse).
  • Interaction Summary page
    • Shows a summary view of all interactions and preys for each bait.
      • Use the Choose a bait pull-down menu to choose a bait. Choose between Bait/Prey/Library or Bait/Prey combination for the interaction summary view. The Bait/Prey/Library option aggregates different cDNA positions for a given prey/library combination. The Bait/Prey option aggregates different libraries and cDNA positions for a given prey. After choosing the options, click on the Update Summary button. The summed-up number of interactions for each combination is shown in the last column.
      • Bait Locus and Prey Locus are linked to its entry in TAIR database for more information.
      • Mouse over a library name to see the description of the library.
  • Bait Specific Interaction Summary page
    • Lists all interactions with preys for a given bait protein. The bait name and TAIR locus are listed at the top along with the number of interactions. Use the buttons above the table to change the view.
      • Sort button changes the table listing order.
      • Show non-redundant prey protein list button shows the non-redundant list of preys regardless of the libraries and cDNA positions.
      • Show all prey protein list button lists all interactions including all combinations of preys, libraries, and cDNA positions. This is the view shown at first. The button toggles with Show non-redundant prey protein list button.
      • Prey Locus is linked to its entry in TAIR database for more information.
      • Use TAIR icon button to visualize TAIR interactome information for the given prey protein. It launches N-Browse Java Applet from TAIR.
      • Use N icon button to visualize our G-signaling interactome information for the given prey protein. It launches N-Browse Java Applet on our server.
      • AtPID link brings up the prey locus information from AtPID.
      • Mouse over a library name to see the description of the library.
  • Preys
    • Lists all prey proteins found to interact with one or more of the baits.
      • Prey Locus is linked to its entry in TAIR database for more information.
      • The button in the Interaction column shows the number of interactions for each prey. See the description below Prey Specific Interaction Summary page.
      • Use TAIR icon button to visualize TAIR interactome information for the given prey protein. It launches N-Browse Java Applet from TAIR.
      • Use N icon button to visualize our G-signaling interactome information for the given prey protein. It launches N-Browse Java Applet on our server.
      • AtPID link brings up the prey locus information from AtPID (Arabidopsis thaliana Protein Interactome Databse).
      • Use the Show preys with pull-down menu to list prey proteins that interact with a certain number of baits. — To be added
  • Prey Specific Interaction Summary page
    • Lists all interactions with baits for a given prey protein. The prey TAIR locus and synonyms are listed at the top along with the number of interactions. Use the buttons above the table to change the view.
      • Show non-redundant bait protein list button shows the non-redundant list of baits regardless of the libraries and cDNA positions.
      • Show all interactions button lists all interactions for the given prey including all combinations of libraries and prey cDNA positions. This is the view shown at first. The button toggles with Show non-redundant bait protein list button.
      • Bait Locus is linked to its entry in TAIR database for more information.
      • Use TAIR icon button to visualize TAIR interactome information for the given prey protein. It launches N-Browse Java Applet from TAIR.
      • Use N icon button to visualize our G-signaling interactome information for the given prey protein. It launches N-Browse Java Applet on our server.
      • AtPID link brings up the prey locus information from AtPID.
      • Mouse over a library name to see the description of the library.
      • Corr Coeff shows the correlation coefficient values — description to be added
  • Interactions
    • Lists all interactions between baits and preys in our G-signaling database.
      • Bait Locus is linked to its entry in TAIR database for more information.
      • Prey Locus is linked to its entry in TAIR database for more information.
      • Corr Coeff shows the correlation coefficient values — description to be added
      • Mouse over a library name to see the description of the library.
  • Search DB
    • Allows users to search through our G-signaling interactome database using names, Locus, and symbols (synonyms) for baits and preys, by choosing the library, or using keywords in the description.
  • Links
    • Contains relevant and useful links.

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cDNA Library Information:

  • The cDNA library information is available from here. A short description of each library can be also viewed by doing mouse-over on any library name in a table.

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Data download:

  • Use the buttons under the tables to download the data in a tab-delimited table format (a text file). The data can be downloaded in two formats. The first table format includes all information as shown in the page. The second table format, called "bait-prey table", includes only two columns, a bait protein name and the prey protein the bait interacts with.
  • See N-Browse description below how to upload the bait-prey table for a graphic presentation.

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N-Browse:

  • It is an open-source interactive graphical browser for biological network, developed originally by Kris Gunsalus and Huey-Ling Kao, currently by Monty Schulman, at New York University (http://www.gnetbrowse.org).
  • We have installed and are running N-Browse2 on our server. Both of TAIR and our interactome data can be visualized with N-Browse by clicking on the TAIR and N icon buttons in the tables or using the links available in the Link page. N-Browse can be run as either Java Applet or Java Web Start. Applet version is launched from the tables, which runs within the Web browser (another Web page will be opened). Java Web Start version is available in the Links page. It starts a Java application on your machine.
  • When you click on the N icon button in a table, it launches N-Browse with the given bait or prey protein as the starting point and shows all proteins that are known to interact with. In the N-Browse window, a new starting gene can be provided in the Search New Gene field. Click on GO button to see the new interaction image.
  • How to overlay our data over TAIR interactome using N-Browse:
    1. Download interaction information as a tab-delimited table format from our database by using Download the bait-prey table button.
    2. Use N-Browse at TAIR link (in the Links page) to launch N-Browse with TAIR interactome.
    3. In N-Browse, use File/Open File menu, choose the file you saved, type in the Starting Point gene name (e.g., Bait name), check Cooperate with DB, and click on Browse button.
  • N-Browse Applet compatibility issues:
    We tested N-Browse Applet (and confirmed it runs) in following OS's and Web browsers:
    • Macintosh OS X 10.6: Google Chrome, Safari (5.0.x, seems to be slower than Chrome)
    • Macintosh OS X 10.5.8: Safari (5.0.x), Google Chrome (5.0.375.125)
    • Macintosh OS X 10.4.11: Safari (4.1.1), FireFox (3.5.11, 3.6.8)
    • Windows XP: Internet Explore, FireFox, Google Chrome
    • Windows Vista: FireFox, Google Chrome
    • Windows 7: Internet Explore, FireFox
  • Depending on the OS and Web browser versions, compatibility may be different. If you have any problem with N-Browse Applet, please try different Web browser.
  • Trying to launch multiple N-Browse Applet does not work very well. You need to close the first N-Browse window before opening another one. If you open one N-Browse window by clicking on an N (or TAIR) icon, close the window before you try to click on another N (or TAIR) icon. You can avoid launching multiple N-Browse Applets by typing in gene name(s) in the Search New Gene field.
  • In N-Browse, you can also type in more than one gene names in the Search New Gene field. This shows you all interactions involved with the given gene set.

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Who we are:

  • Arabidopsis G-Signaling Database Development Group
    • Dr. Etsuko N. Moriyama (University of Nebraska - Lincoln)
    • Brandon Fulk (Web development, Undergraduate, University of Nebraska - Lincoln)
    • Kelsey Augustin (Former Web programmer, Undergraduate, Nebraska INBRE Scholar, Wayne State College)
    • The Nguyen (System Administrator, Professional Computer Solutions)
  • Arabidopsis G-Signaling Interactome Research Group
    • Dr. Alan M. Jones (University of North Carolina at Chapel Hill)
    • Dr. John Schwarz (University of North Carolina at Chapel Hill)
    • Dr. Joachim F. Uhrig (University of Cologne, Germany)
    • Dr. Karsten Klopffleisch (University of Cologne, Germany)
    • Dr. Ralph Panstruga (Max-Planck Institute)
    • Matthew Tan Chong Yang (Undergraduate, National University of Singapore)
  • [ Data source files ]

Publications:

  • Klopffleisch, K., Phan, N., Augustin, K., Bayne, R. S., Booker, K. S., Botella, J. R., Carpita, N. C., Carr, T., Chen, J.-G., Cooke, T. R., Frick-Cheng, A., Friedman, E. J., Fulk, B., Hahn, M. G., Jiang, K., Jorda, L., Kruppe, L., Liu, C., Lorek, J., McCann, M. C., Molina, A., Moriyama, E. N., Mukhtar, M. S., Mudgil, Y., Pattathil, S., Schwarz, J., Seta, S., Tan, M., Temp, U., Trusov, Y., Urano, D., Welter, B., Yang, J., Panstruga, R., Uhrig, J. F. and Jones, A. M. (2011) Arabidopsis G protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Molecular Systems Biology 7: 532.

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Funds:


Acknowledgements:

  • We thank Monty Schulman for his kind help for trouble-shooting installing N-Browse2 on our local server.