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Filamentous Fungal Gene Expression Database
Frequently Asked Questions

  FAQ

Answers to some of the most frequently asked questions submitted to FFGED are listed as follows.

  1. Introduction
    1. What is FFGED?
    2. How do I submit an experiment to the database?
    3. How do I cite FFGED?
  2. FFGED Accounts
    1. How do I acquire a FFGED account?
    2. Do I need to register a FFGED account if I only want to do normalization?
    3. How do I update my account information or change password?
    4. I've forgotten my FFGED username and password?
    5. I can't log into FFGED?
  3. Data Entry
    1. How do I get started?
    2. Experimental metadata
    3. Experimental variables
    4. GPR
    5. Normalization
    6. Analyzed results
  4. Public Experiments
    1. What are public experiments?
    2. How do I access public experiments? If I am interested in one of them, how can I contact the submitter?
    3. Related Experiments are all public experiments?
  5. Public Results
    1. What are public results?
    2. How do I access public results?
    3. Can public results be exchanged with other institutions?
    4. Can gene expression public results be embedded into any web site?
  6. Data and Database Help
    1. Online Feedback
    2. Contact Us


  1. Introduction

    1. What is FFGED?

      FFGED (Filamentous Fungal Gene Expression Database) is an "active experiment" database, allowing users to submit experiments, in which users can define experimental metadata, design experimental variables for cy3/5 treatment, upload GPR files, normalize online or upload normalized data, generate pre-BAGEL file and upload analyzed results.

      As a consequence, several web tools have been incorporated into FFGED, including online normalization, online annotation, generation of pre-BAGEL files for analysis and automated plotting of expression measure figures.

      In FFGED, each experiment can be set public or private to one or several users, facilitating data sharing and collaborative work at different sites.

    2. How do I submit an experiment to the database?

      To submit an experiment, you may easily take the following directions step by step:

      • Enter experiment metadata
      • Design experiment
      • Upload raw data
      • Normalize raw data (modified from Normalization Excel Template for GenePix) OR upload your normalized data
      • Upload analysis results
    3. How do I cite FFGED?

      The citation for FFGED is: Zhang, Z. and J.P. Townsend. The filamentous fungal gene expression database (FFGED). Fungal Genet Biol. 2009 Dec 16. [Epub ahead of print]

      Please see here for a list of publications related to FFGED.

  2. Accounts

    1. How do I acquire a FFGED Account?

      Any user can freely register and get the FFGED account. As soon as your registration is submitted, your account will be opened and you will receive an e-mail with your username and password.

    2. Do I need to register a FFGED account if I only want to do normalization?

      Not necessary. Users can do normalization online, without requirement of registeration.

    3. How do I update my account information or change password?

      To update your account information, you need to log on the database. Then you may find a link named "Update my information" at the top right or click here to change password or update contact details.

    4. I've forgotten my FFGED username and password.

      • If you are already a member, but have forgotten your password, you may find the password by clicking here. The password will be sent to you as an e-mail.
      • Contact us using the feedback page.
    5. I can't log into FFGED?

      • Make sure that the Caps Lock key is not depressed. Login names are not case sensitive, but passwords are.

      • Make sure your browser is set to accept cookies. It's usually in the "Advanced" subcategory under the "Preferences" menu in both IE and Netscape.

      • Contact us using the feedback page.

  3. Data Entry

    1. How do I get started?

      • Entering an experiment requires that you log on the database, so you need to register an account if you are not a member.
      • Please note that fields marked ** are required when submitting experiments.

    2. Experimental metadata

      • Enter experimental metadata to describe your experiment, including name of experiment, experimental description, citations, publication link, abstract, keywords and date for public experiment.

      • Please refer to the FFGED Experiment Access FAQs for additional information on Private Experiments Vs. Public Experiments.

    3. Experimental variables

      • Enter experimental variables to design your experiment, including variable name, dimension, type, unit, values and descriptions.

      • Experimental variables are correlated to cy3/5 treatments and related experiments depend on what kind of variables you input and how many they are.

      • Please refer to the FFGED Account FAQs for additional information on Related Experiments.

    4. Raw Data

      • Upload raw data files, with GenePix Results (GPR) or CSV files (.gpr/csv required).

      • Three files can be uploaded at one time.

      • Please note that input files following the format with required fields can be normailzed online.

    5. Normalized Details

      • Normalize online using the method 'Townsend, Cavalieri and Hartl (2003)': choose one from uploaded GPR files and set experimental variables' values for cy3/5 treatment.

      • OR upload normalized file and choose experimental variables' values for cy3/5 treatment.

      • Please note that each normalized file should be associated with specific experimental variables.

    6. Analysis Results

      • Generate pre-BAGEL (Bayesian Analysis of Gene Expression Levels) file for the statistical analysis of spotted microarray data.

      • More information about BAGEL can be found at here.

      • Upload analysis results files and associate expression levels with experimental variables.

  4. Public Experiments

    1. What are public experiments?

      Contrary to private experiments that are accessed only by author, public experiments can be accessed by any one. Any experiment submitted to FFGED, can be searched related experiments within the scope of public experiments.

      The purpose of public experiments is to increase communications and collaborations among different users.

    2. How do I access public experiments? If I am interested in one of them, how can I contact the submitter?

      Any user can access public experiments on the page of "Public Data". If interested, you can just click the submitter's email address.

    3. Related Experiments are all public experiments?

      Yes. User can set experiment public or private when entering experimenal metadata. For each experiment, FFGED only searches public experiments for related experiments.

      Related experiments are listed accroding to similarity from high to low.

  5. Public Results

    1. What are public results?

      Public results are gene expression levels with detailed experimental variables, which are all extracted from result files in public experiments.

      The purpose of public results is to harness collective intelligence for knowledge discovery, which is one of applications in Bringing Web 2.0 to bioinformatics. Therefore, we encourage to make your gene expression experiments public.

    2. Can do I access public results?

      Any user can access public results on the page of "Public Data".

    3. Can public results be exchanged with other institutions?

      Yes. Data sharing is of great significane to discover knowledge, especially for data-intensive biological studies. An XML (Extensible Markup Language) retrieval mode is provided for data exchange.

      Base URL: http://bioinfo.townsend.yale.edu/xml/esearch_expression.jsp?

      URL Parameter: gene - Neurospora crassa gene name

      Example: retrieve records for NCU01101 in XML mode

      http://bioinfo.townsend.yale.edu/xml/esearch_expression.jsp?gene=NCU01101

    4. Can gene expression public results be embedded into any web site?

      Yes. FFGED offers a dynamic interface to embed up-to-the-minute experimental results for the expression of a relevant gene into any web site.

      Example: Expression information of gene NCU09997 is embedded in the Broad Institute website.

      http://www.broadinstitute.org/annotation/genome/neurospora/GeneLocus.html?sp=SNCU09997

      How to embed: http://bioinfo.townsend.yale.edu/browse_results.jsp?gene=NCU09997

  6. Data and Database Help

    1. Online Feedback

      Please send suggestions or comments using online feedback.

    2. Contact Us

      For any questions or potential collaboration, please find our contact information here to contact us.