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GNCPro FAQ

Table of Contents
  1. What is GNCPro?
  2. What can GNCPro do for researchers like me?
  3. How can I start using GNCPro
  4. Does GNCPro support a "wild-card" search like Google?
  5. How is the GNCPro service implemented?
  6. What do I need to run the GNCPro program?
  7. How do I get the latest version of the JRE on my computer?
  8. My Mac computer tells me that I already have the latest version of JRE, but why do I still get an error message, and why am I still unable to see a graph?
  9. Can I upload gene expression fold-changes and other data for my GOI into GNCPro?
  10. How can I get a cleaner picture?
  11. Why do some gene symbols have a '#' in the middle?
  12. What does "co-expression" mean?
  13. I clicked an option in the network graph, but why I didn't I see the resulting change?
  14. How can I save my data?
  15. Can I save my job today and continue it later?
  16. Can I upload my data using an Excel file?
  17. What does the "Relax" button on the graph do?
  18. What is the difference between SVG and Medusa?
  19. What species are supported by GNCPro?
  20. In a network view, how are the "Tissue-Specific Associations" determined?
  21. What is the purpose of the "Edge Color" checkbox?
  22. Why do I get an error saying "Cannot expand node more than 4 times" when I try to "Get More Neighbors" or "Too many genes to process" when I try to "Expand Graph"? Are there any limitations to "Expand Graph" or "Get More Neighbors"?
  23. Is there any significance to the gene (node) positions or the length of the interactions (edges) between genes? How are they interpreted?
  24. How can I more easily visualize directionality between genes?


  1. What is GNCPro?

    GNCPro, free online software developed and maintained by SABiosciences, is an in silico research tool for collating gene and pathway interactions. GNCPro integrates collective biological knowledge through text mining, data mining, data acquisition and computational prediction. The interactions among a group of genes are represented graphically and are interactive. In addition to predetermined lists of biological pathways and processes, you can also view the interactions among your genes of interest.

  2. What can GNCPro do for researchers like me?

    GNCPro can help researchers:

    • Identify genes that are functionally related to their genes of interest (GOI)
    • Identify potential candidates that bridge the gaps in their biological pathways
    • Find interactions that can define better experiments or better drug targets
    • View their own data against existing discoveries, and view custom data in network graphs
    • Navigate biological knowledge graphically

  3. How can I start using the GNCPro?

    There are five ways to feed genes into the GNCPro program:

    • Input a list of genes (or a single gene) by manually typing or pasting into a window or by uploading a text file.
    • Choose a pathway from one of three drop-down menus
    • Choose a Gene Ontology term by searching for a term or ID or by navigating menu trees
    • Choose a human disease term
    • Retrieve a previously saved job identified by its job ID

    The submitted gene list will then be displayed as a network graph.

  4. Does GNCPro support a "wild-card" search like Google?

    Yes. For example, if you type "leu" when searching for a Human Disease, all the following disease terms will appear. Simply mouse-over and click the desired term.

    acute leukemia
    acute lymphoblastic leukemia
    acute myeloblastic leukemia
    acute myelogenous leukemia
    acute myeloid leukemia
    acute non-lymphocytic leukemia
    acute nonlymphocytic leukemia
    acute promyelocytic leukemia
    acute tscell leukemia
    acute-lymphocytic leukemia
    adult acute leukemia
    adult tscell leukemia
    b-chronic lymphocytic leukemia
    bscell chronic lymphocytic leukemia
    bscell leukemia
  5. How is the GNCPro service implemented?

    The GNCPro is implemented as a classic three-tier structure. In the front tier is the graphic user interface embedded in the web browser. The back-end is a mySQL database where the data is stored. In the middle, lies the web server that takes queries from the users and fetches data from the database, which is then passed to the user.

  6. What do I need to run the GNCPro program?

    For its most useful, interactive, and sophisticated features, the software requires the Java run time environment (JRE) version 1.5 or higher. Alternatively, you can use the SVG Viewer plug-in; however, the capabilities of the software will be more limited.

  7. How do I get the latest version of the JRE on my computer?

    You can download JRE 1.5 here.

  8. My Mac computer tells me that I already have the latest version of JRE, but why do I still get an error message, and why am I still unable to see a graph?

    Unfortunately, in Mac computers, the operating systems and Java run time environment are tied together. You can only get some JRE versions for your version of Mac OS, and not necessarily the absolutely latest one offered by the Sun Microsystems. You will need to up-date your Mac OS in order to actually install the most recent JRE version.

  9. Can I upload gene expression fold-changes and other data for my GOI into GNCPro?

    Currently, this feature is unavailable. However, newer versions of this software may include it.

  10. How can I get a cleaner picture?

    If you feel that your graph is too messy, you can get a cleaner picture by:

    • Removing genes from the graph unrelated to the relationships or genes of interest
    • Clicking and dragging nodes around to move them away from one another
    • Selectively displaying only those relationships of interest to you

  11. Why do some gene symbols have a '#' in the middle?

    Sometimes, the same aliases or synonyms are shared by different genes. Our text-mining algorithm cannot determine specifically which of those genes is referenced in the paper at this time. Consequently, the software displays all of the possible genes, separated by '#', that may actually be the gene relevant to the network. Efforts are ongoing to improve the algorithm's ability to make distinctions between genes with similarly redundant nomenclature.

  12. What does "co-expression" mean?

    "Co-expression" means that two genes have similar expression profiles or are expressed at the same time in the same model system, as determined by multiple experiments.

  13. I clicked an option in the network graph, but why I didn't I see the resulting change?

    You may have a pop-up blocker enforced in your internet browser. Take the appropriate action to unblock pop-up windows when using GNCPro.

  14. How can I save my data?

    The work that you perform in each session data is saved automatically onto our server. However, if you are not logged into your account on GNCPro, your data will only be stored for as long as the browser window is open. Once the browser window is closed, the data will be removed from the server. If you are logged into your account on GNCPro, your data will still be saved on our server regardless of whether you close the session, and you may return to your work at a later session upon logging in again.

  15. Can I save my job today and continue it later?

    If you are logged in, your job will be automatically saved into the database. You can continue this job later. However, any graph manipulations that you've done will not be saved. In the future, this may become a possible feature, depending on user demand.

  16. Can I upload my data using an Excel file?

    Currently, this feature is unavailable. Gene lists must be uploaded in plain text format at this time. However, newer versions of this software will support Excel file uploads.

  17. What does the "Relax" button on the graph do?

    The "Relax" button implements a spring layout where genes are pushed together or pulled apart from one another based on a calculation of the sum total of the force of their total associations with each other. The "Relax" button enhances visualization by emphasizing those clusters of closely-interacting genes.

  18. What is the difference between SVG and Medusa?

    The SVG gene network automatically optimizes its layout, but is static and not interactive, and its image can only be saved by using the internet browser software to right-click on the image and select the "Save Image As" feature. However, SVG is a vector-based image layout that can be edited by a variety of image editors that support the SVG image format, and it is not prone to being blocked by firewalls as Java applets are.

    The Medusa gene network is fully interactive requiring you to optimize the layout, and its image may be exported and saved as either a JPEG or PNG formatted file. However, it also requires Java run time environment to take advantage of all of its functionality.

  19. What species are supported by GNCPro?

    Currently, GNCPro only supports networks among human genes.

  20. In a network view, how are the "Tissue-Specific Associations" determined?

    If at least one probe from one of the datasets used for the "Tissue Expression Viewer" for a given gene shows significant gene expression in a selected tissue, then that gene is considered to be expressed in that tissue.

  21. What is the purpose of the "Edge Color" checkbox?

    Deselecting the "Edge Color" feature, provided by the Java platform, creates a simpler version of the network graph displaying only single interactions (edges) between genes (nodes). However, the interaction details between genes will be lost when "Edge Color" is deselected, while reselecting this feature brings them back.

  22. Why do I get an error saying "Cannot expand node more than 4 times" when I try to "Get More Neighbors" or "Too many genes to process" when I try to "Expand Graph"? Are there any limitations to "Expand Graph" or "Get More Neighbors"?

    There are limitations to "Expand Graph" and "Get More Neighbors". In order keep the network view relatively interpretable, the software will only allow you to "Get More Neighbors" up to four times for a specific node (gene) and add a maximum number of 100 genes per network using either "Get More Neighbors" or "Expand Graph."

  23. Is there any significance to the gene (node) positions or the length of the interactions (edges) between genes? How are they interpreted?

    There is no significance to the edge lengths or node positions, unless the "Relax" feature is activated. The "Relax" feature clusters the genes according to the strength of their interactions. The length of the edges are inversely proportional to the strength of the interaction between genes; that is, the stronger the gene-gene interaction, the shorter the edge length.

  24. How can I more easily visualize directionality between genes?

    If directionality exists in the relationship (edge) between genes (nodes), a directional arrow is displayed and can be more easily viewed by repeatedly deselecting / reselecting the "Directed" option at the top of the network graph.



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