GeneInfoViz: Constructing and Visualizing Gene Relation Networks

Table of Contents

  1. What is GeneInfoViz?
  2. How to use GeneInfoViz?
  3. When was GeneInfoViz last updated?
  4. How to cite GeneInfoViz?
  5. Contact us

What is GeneInfoViz?

GeneInfoViz is a web based tool for gene relation analysis and visualization. It takes a list of genes as input, and returns a table containing the gene function information retrieved from LocusLink, GeneBank and GeneOntology databases. GeneInfoViz also provides two kinds of visualization of the relations between the genes - One displays part of the Gene Ontology DAG( Directed Acyclic Graph) that is associated with the input genes; the other shows the gene relation network.

How to use GeneInfoViz?

  • To see a demo:
    1. Select Human
    2. Select to search by LocusID
    3. Click on "Sample Gene List"
    4. Select the evidence codes of your interest
    5. Click on "Search"

  • Use your own list of genes as input:
    1. Select an organism
    2. Enter your gene list, entries in the list must be seperated by space or new-line character
    3. Select to search by Locus ID, UniGene ID, Accession Number or Symbol
    4. Select the evidence codes
    5. Click on search

  • Information about the genes, such as UniGeneID, Gene Ontology Term and Type, Gene Symbol will be listed in a table, which we call it gene-info-table.

  • Above the gene-info-table, you will see 3 buttons that read as "Directed Acyclic Graph", each of them represent a Gene Ontology Type: Biological Process, Molecular Function or Cellular Component. Click on one of them, its corresponding DAG graph will appear in a new window.

  • There are another 3 buttons, read as "Biological Process", "Molecular Function" and "Cellular Component". Next to them, is the drop down menu of "levels" which refers to the level in the DAG graph. Select a level, click on one of these buttons, a gene-relation-networks graph will be displayed.

  • You can check box "distance" to show the lengths of the edges; you can also use mouse to drag the genes to adjust their postions in the graph. Click on the hypertext links, you can see the Adjacency Matrix, Distance Matrix and Indicator Table.

    When was GeneInfoViz last updated?

    The database of GeneInfoViz was last updataed 7/7/05.

    How to cite GeneInfoViz?

    To reference GeneInfoViz, please cite this paper:
    Mi Zhou and Yan Cui (2004) GeneInfoViz: Constructing and visualizing gene relation networks. In Silico Biology Vol.4 0026


    Please send questions and comments to Dr. Yan Cui at University of Tennesee Health Science Center.

    Developed and maintained by Yan Cui's Lab at University of Tennessee Health Science Center