GEDI v2.1 DEMO

Please click the following links for animated demonstrations of GEDI’s major functionalities. The data file used in the demo can be downloaded from here.

  • Start a new GEDI analysis, save the session.
  • Load a GEDI session, and navigate through GEDI.
  • Static analysis and Dynamic analysis.
  • Display selected samples, and calculate average or difference.
      

    • Examples of gene expression profiles time courses as movies generated using GEDI

    The GEDI program presents time courses of gene expression profiles as movies and allows for the discovery of patterns through a new and intuitive format. (Eichler G. S., Huang S., Ingber D.E., Bioinformatics, 2003 Nov 22;19(17):2321-2).

     

    Slime Mold Development

    Download the movie of Slime Mold Differentiation
    The data for this movie is taken over a 24 hour period, with time points measured at regular 2 hour intervals. The 19 X 18-tile mosaic represent 2022 genes. Note the drastic change of the global pattern (corresponding to a large jump in gene expression state space) at 6 hours (approximately 1/4 into the movie). This event correlates with the phenotypic transition from a unicellular to a multicellular stage during slime mold development.

    This data was published in:
    Van Driessche N., Shaw, C., Katoh, M., Morio, T., Sucgang, R., Ibarra, M., Kuwayama, H., Saito, T., Urushihara, H., Maeda, M., Takeuchi, I., Ochiai, H., Eaton, W., Tollett, J., Halter, J., Kuspa, A., Tanaka, Y. and Shaulsky, G. (2002). A transcriptional profile of multicellular development in Dictyostelium discoideum, Development, 129,1543-1552

    Cell Cycle

    This movie (25 X 25-tile mosaic) visualizes the expression of 967 genes that exhibit cyclic expression values in the HeLa Cell Cycle over a 46 hour period, sampled every hour. The phase shifted and cyclic behavior of genes of individual gene clusters is immedately apparent as a global rotation of the patterns. The decay of the ordered patterns is due to the desynchronization of the cell cycle.

    This data was published in:
    Whitfield M., Sherlock G., Saldanha A. J., Murray J. I., Ball C. A., Alexander K. E., Matese J. C., Perou C. M., Hurt M. M., Brown P. O., Botstein D. (2002). Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors, Molecular Biology of the Cell, 13, 1977-2000

    HL60 Differentiation

    This movie shows 3683 genes in two parallel time courses of cells undergoing HL60 differentiation into neutrophil-like cells with either retinoic acid (on the left side of the movie) or dimethylsulfoxide (on the right side of the movie). The time courses cover a period of 6 days (12 samples with higher sampling density during the first day). Note the drastic difference in the expression profiles during the first quarter of the movie and the ensuing convergence towards similar expression patterns supporting the attractor hypothesis.
    The "slug-like" migration of islands of activation or deactivation which correspond to clusters of genes represent a temporal sequence of gene expression. This might suggest the existence of regulatory cascades.

    A similar set of data has been used in this paper: Huang S., Eichler, G. S., Bar-Yam, Y., and Ingber, D.E. (2005) Cell fate as high-dimensional attractor of a complex gene regulatory network. Physics Review Letters. 94(12): 128701, 2005.
     

    Static Visualizations of Normal Human Tissues

    This static GEDI visualization represents various healthy tissues from 18 different donors. The microarrays measured 7035 genes in this experiment. Note the distinct patterns of gene expression found in each of the tissue types, creating differentiable yet robust patterns for each tissue type. Interestingly, there was a noticeable difference between male and female muscle.
     

    This data was published in the paper:
    Haverty, PM., Weng, Z., Best, N., Auerbach, K., Hsiao, L., Jensen, R., Gullans, SR. HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Research 30: 214-217, 2002.