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Overview

High-Throughput GoMiner™ generates files that are useful for cluster analysis. The purpose of these instructions is to facilitate construction of clustered image maps (CIMs) using CIMminer so that users can both replicate the cluster images found in the High-Throughput GoMiner manuscript, and create similar CIMs constructed from their own data. Note that the current version of HTGM will generate CIM's automatically if CIM generation is selected, and there is sufficient data for the image. This instructions remain here for users who want to understand the process to tailor it.

Browser Requirements

Specific Instructions for Figure 3 of the High-Throughput GoMiner manuscript

We refer to CIMs similar to Figure 3 as “trinary” because they contain exactly three values. In particular, the values are -1, 0, and 1.

  1. Start with the input file, CHANGEDGENESFILE.change.gce.updown.CIM which is described in Output Files.
  2. If you are using a Mac, make sure the file ends in '.txt'. Screenshot of file submission in CIMminer
  3. On the following section, select the following clustering options, as shown here:
    Clustering
    Screenshot of algorithm selection in CIMminer
  4. This will generate an initial CIM. Select Colors and adjust the all of the display options for Colors, Page Layout and Axes, and then press Redraw.
    1. Colors
      Screenshot of color selection in CIMminer
    2. Page Layout
      Screenshot of page layout selection in CIMminer
    3. Axes
      Screenshot of axis labeling in CIMminer
  5. This will generate a new CIM. Save this CIM as .gif. Right-click (Control Click on a Mac) to reveal menu and select “Download Image to Disk.” This menu item may be phrased differently on your browser.
    Example clustered image map generated from CIMminer for a single changed file

Specific Instructions for Figure 4 of the High-Throughput GoMiner manuscript

We refer to CIMs similar to Figure 4 as “continuous” because the entries can assume any floating point values. In this particular instance, the values are all non-negative.

  1. Start with the input file, total.txt.change.series.CIM which is described in Output Files.
  2. If you are using a Mac, make sure the file ends in '.txt'. Screenshot of file submission in CIMminer
  3. On the following section, select the following clustering options, as shown here:
    Clustering
    Screenshot of algorithm selection in CIMminer
  4. This will generate an initial CIM. Select Colors and adjust the all of the display options for Colors, Binning, Page Layout and Axes, and then press Redraw.
    1. Colors
      Screenshot of color selection in CIMminer
    2. Binning
      Screenshot of binning algorithm selection in CIMminer
    3. Page Layout
      Screenshot of page layout selection in CIMminer
    4. Axes
      Screenshot of axis labeling in CIMminer
  5. This will generate a new CIM. Save this CIM as .gif. Right-click (Control Click on a Mac) to reveal menu and select “Download Image to Disk.” This menu item may be phrased differently on your browser.
    Example clustered image map generated from CIMminer for multiple changed files

Pitfalls


GoMiner™ is a development of the Genomics and Bioinformatics Group, Developmental Therapeutics Branch (DTB), Developmental Therapeutics Program (DTP), Center for Cancer Research (CCR), National Cancer Institute (NCI). We would like to hear from you. You can reach the team via email.

GoMiner was originally developed jointly by the Genomics and Bioinformatics Group (GBG) of LMP, NCI, NIH and the Medical Informatics and Bioimaging group of BME, Georgia Tech/Emory University. It is now maintained and under continuing development by GBG.

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