Figure 3. Gene expression in different tissues


a. Fold reduction or induction of unique transcripts for each of the comparisons analyzed. The source of the transcripts included in each comparison are displayed in 2c. The relative expression of each transcript was determined by dividing the number of transcript tags in each comparison in the order displayed in 2c. To avoid division by 0, we used a tag value of 1 for any tag that was not detectable in one of the samples. We then rounded these ratios to the nearest integer; their distribution is plotted on the X axis. The number of transcripts displaying each ratio is plotted on the Y axis. Each comparison is represented by a specific color (see below or 3c).

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b, Expression of transcripts for each comparison, where values on X and Y axes represent the observed transcript tag abundances in each of the two compared sets. Light Blue symbols: DLD1 in different physiologic conditions; Yellow symbols: DLD1 cells (X axis) versus HCT116 cells (Y axis); Red symbols: colon cancer cells (X axis) versus normal brain (Y axis); and Dark Blue symbols: colon cancer cells (X axis) versus hemangiopericytoma (Y axis).

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c, Fraction of transcripts with dramatically altered expression. For each comparison, Expression Change denotes the number of transcripts induced or reduced 10 fold, and (%) denotes the number of altered transcripts divided by the number of unique transcripts in each case. Differences between expression changes were evaluated using the chi squared test, where the expected expression changes were assumed to be the average expression change for any two comparisons.




Total Transcripts

Unique Transcripts

Expression change >= 10 fold (%)


DLD1 condition A vs DLD1 condition B



43 (0.10)


DLD1 vs HCT116



390 (0.70)A


Colon Cancer vs Normal Brain



930 (1.49)B


Colon Cancer vs Hemangiopericytoma



1,047 (1.45)C

A Difference between expression change of comparison 1 and 2, p < 0.0001

B Difference between expression change of comparison 2 and 3, p < 0.0001

C Difference between expression change of comparison 2 and 4, p < 0 .0001


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