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This observation poses a problem in validating gene expression microarray signatures related to EMT because the overall tumor genetic make-up probably masks these rare events.
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Various gene signatures related to the survival and recurrence of hepatocellular carcinoma (HCC) have been identified using microarray analysis, and proposed to supplement clinicopathological prognostic factors for prediction of patient outcomes [ 1- 4].
We also investigated proteomic signatures related to antidepressant treatment response32.
The overall main effect of age on microarray signatures, however, was clearly detectable and was subjected to further analysis.
Only three genes were shared between the two microarray signatures.
This procedure identified RGS4, MCTP1, CD44 and XIST as common between the two microarray signatures.
It has previously been described that proteins not selected as part of signatures in microarray experiments were related to disease due to its inclusion into a network of PPIs [25], [26].
In contrast, similar studies conducted with these cell lines in vitro did not show induction of the pathway suggesting that in the tumor context additional factors such as those related to immune modulation may contribute to the observed microarray signature.
The 70-gene microarray signature was superior to clinicopathological risk assessment in predicting all endpoints.
Specifically, we identified three mutagen-driven signatures, three DNA-repair related signatures, and one recurrent signature with C → T mutations at non-CpG island (CGI) regions.
In addition, various microarray studies have generated genetic signatures of metastasis related to risk [ 7, 8], clinical outcome [ 9] and distant recurrence [ 10], and have identified candidates for targeted therapy [ 11- 13].
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