Difference between revisions of "MRA-FET"
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| − | + | =FET method details= | |
| + | ==Description== | ||
| + | Two choices are available in how to apply the FET method. | ||
| + | * '''One FET run''' - a single run of FET is used to determine enrichment of the signature markers in the hub's regulon. | ||
| + | * '''Two FET runs''' - The data is divided into two subsets based on | ||
| + | ** positive or negative differential expression of targets, and also into two orthogonal subsets based on | ||
| + | ** positive or negative Spearman's Correlation of the expression of the targets across all arrays (not just those used in the test of differential expression) as compared to the hub markers. | ||
| + | |||
| + | ==TF Activity Modes== | ||
| + | |||
| + | Using the notation (differential expression result, Spearman's correlation result) for the intersection of differential expression (+ or -) and correlation (+ or -) results, the following two sets are formed and FET is run for each: | ||
| + | * '''Test 1 (plus mode)''': (+,+) union (-,-). | ||
| + | * '''Test 2 (minus mode)''': (+,-) union (-,+). | ||
| + | |||
| + | Whichever of the two tests gives the more significant p-value is used as the final p-value and the mode is called as "plus" or "minus" correspondingly. The mode is displayed in the MRA results viewer. | ||
| + | |||
| + | ==Simplified Interpretation of Modes== | ||
| + | * '''Plus mode''' - the expression profile of the TF is positively correlated with those of regulon markers showing positive differential expression in the "case" set. The TF is more active in the "case" state. | ||
| + | * '''Minus mode''' - the expression profile of the TF is positively correlated with those of regulon markers showing negative differential expression in the "case" set. The TF is more active in the "control" state. | ||
Revision as of 14:26, 26 November 2012
Contents
FET method details
Description
Two choices are available in how to apply the FET method.
- One FET run - a single run of FET is used to determine enrichment of the signature markers in the hub's regulon.
- Two FET runs - The data is divided into two subsets based on
- positive or negative differential expression of targets, and also into two orthogonal subsets based on
- positive or negative Spearman's Correlation of the expression of the targets across all arrays (not just those used in the test of differential expression) as compared to the hub markers.
TF Activity Modes
Using the notation (differential expression result, Spearman's correlation result) for the intersection of differential expression (+ or -) and correlation (+ or -) results, the following two sets are formed and FET is run for each:
- Test 1 (plus mode): (+,+) union (-,-).
- Test 2 (minus mode): (+,-) union (-,+).
Whichever of the two tests gives the more significant p-value is used as the final p-value and the mode is called as "plus" or "minus" correspondingly. The mode is displayed in the MRA results viewer.
Simplified Interpretation of Modes
- Plus mode - the expression profile of the TF is positively correlated with those of regulon markers showing positive differential expression in the "case" set. The TF is more active in the "case" state.
- Minus mode - the expression profile of the TF is positively correlated with those of regulon markers showing negative differential expression in the "case" set. The TF is more active in the "control" state.
