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I am working with a network object where the nodes are different events in molecular biology.

Specifically; Catalytic activity of X, RNA expression of X, GTP-bound activity of X, Kinase activity of X, Oxidoreductase activity of X, Phosphatase axtivity of X, Transcriptional activity of X, Phosphorylation at residue Y.

What is the difference between RNA expression and Transcriptional activity? And which is the one that an Affymetrix microarray is measuring? eg.; transcriptional activity of KLF2, transcriptional activity of ATF2 RNA expression of HSPA1A RNA, and expression of CYP1B1

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I'm not familiar with what you're doing, but off the top of my head I'd say that the RNA Expression might be referring to everything post-nucleus in that the Introns are missing. The Transcriptase would show more activity because it would still Transcribe both Introns and Exons. –  MCM Feb 20 '13 at 12:55
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In your case, RNA expression and transcriptional activity probably differ in the stage of processing. Transcriptional activity refers to the binding and processive activity of RNA polymerase. There are different ways to measure this experimentally, but with a microarray you are measuring the amount of actual transcripts relative to the control array.

RNA expression usually refers to the amount of mature transcripts but is often used interchangeably with transcriptional activity. The distinction is made at the sample extraction stage and whether or not the RNA was selectively recovered using poly-A selection or other methods that isolate mature transcripts.

What your microarray will measure depends on the probe library constructed on the array and whether you are applying total RNA or selective RNA. Probes matching mature transcripts report for RNA expression. Probes matching immature or nascent transcripts can be used to measure transcriptional activity.

Careful probe design is required to distinguish between the different levels of processing.

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