ArrayStar

Thumbnail Line Graph

ArrayStar’s Line Graph Thumbnails view displays a series of Line Graphs generated from a clustering. Information obtained from the plots helps identify expression patterns with monitored clustering.

Each individual Line Graph shows a visualization of the data contained within one cluster. Expression levels are plotted vertically along the Y-axis, while the X-axis position for each point is determined by the experiment to which it belongs. Mouse-over a vertical gridline to view the experiment name.
Key Features of the Thumbnail Graph are:

  • The number of clusters is automatically determined but users can easily override and define the number they want to see
  • One or more clusters can be selected and then re-clustered to aid in further teasing apart potential regulatory connections.
  • Images can be Copied for use elsewhere such as Microsoft™ Word, etc.
  • Either Absolute or Relative scales can be shown on the graphs
  • Colors of the graphs can easily be changed to meet user requirements

    • scatterplot

    As with other functional images on ArrayStar, an Information Pane is provided to the right of the images.The Information Pane provides users with the following information automatically:

    A.       Overview

    Information provided includes:

  • Clustering method used
  • The distance metric used
  • The number of clusters
  • The number of data points shown
  • The number of tree nodes
  • The tree depth

    • B.       Details

    The Details section of the Line Graph Thumbnails Info Pane displays information about the genes displayed in your clustering. If no genes are selected, the Details section will list the total number of genes in the clustering, as well as the corresponding experiment names.

    If only one cluster is selected, details for the selected cluster will be displayed, including how many genes are in the cluster, as well as the number that are currently selected. Any notes that the user has entered for the cluster will also be displayed.

    If more than one cluster is selected, the Details section will display the number of clusters selected, as well as the total number of genes in the selection.
    If one gene from a cluster is selected, the following information on it will be shown in this section:

  • Gene ontology information
  • The public identification number
  • The gene title
  • The gene symbol

    • C.       Actions

    Recommendations for further analytical actions that the user may want to perform. These include:

  • Showing a Heat Map of the particular clustering
  • Remembering the clustering result
  • Remembering the selection as a gene set
  • Showing the table of selected genes