text: user734: I have seen one of Cellminer tools. I am not sure how do they calculate the cross correlation of the genes, what does it actually mean? Based on what databases? 
  For example if I take their example input (HUGO format): 
  abcb1
  BRCA2
  CNBP
  
  I get the following cross correlation matrix (based on what signals).
  Identifier      abcb1   BRCA2   CNBP
  abcb1           1      -0.142   0.069
  BRCA2          -0.142   1       0.176
  CNBP           0.069    0.176   1
  
  
  user48: In the article describing Cellminer says about the cross-correlations:
  
  ... a cross-correlation table of the resultant z-scores can be
    generated ...
  
  On page 3503
  And the z-scores are defined previously as:
  
  The tool output includes relative transcript intensity presented
    as z-scores...
  
  
original_text: 734: <p>I have seen one of <a href="https://discover.nci.nih.gov/cellminer/" rel="nofollow noreferrer">Cellminer tools</a>. I am not sure how do they calculate the cross correlation of the genes, what does it actually mean? Based on what databases? </p>
  
  <p>For example if I take their example input (<a href="http://www.genenames.org/" rel="nofollow noreferrer">HUGO</a> format): </p>
  
  <pre><code>abcb1
  BRCA2
  CNBP
  </code></pre>
  
  <p>I get the following cross correlation matrix (based on what signals).</p>
  
  <pre><code>Identifier      abcb1   BRCA2   CNBP
  abcb1           1      -0.142   0.069
  BRCA2          -0.142   1       0.176
  CNBP           0.069    0.176   1
  </code></pre>
   48: <p>In the <a href="http://cancerres.aacrjournals.org/content/72/14/3499.full" rel="nofollow noreferrer">article</a> describing Cellminer says about the cross-correlations:</p>
  
  <blockquote>
    <p>... a cross-correlation table of the resultant z-scores can be
    generated ...</p>
  </blockquote>
  
  <p>On page 3503</p>
  
  <p>And the z-scores are defined previously as:</p>
  
  <blockquote>
    <p>The tool output includes relative transcript intensity presented
    as z-scores...</p>
  </blockquote>
  