| These analyses apply different criteria of spot selection such as overexpression, underexpression, maximum and minimum of metagene expression. Additionaly, mutual correlations between the metagenes and k-means clustering was applied to define spots of co-regulated metagenes. Gene set enrichment analysis provides the leading sets of each of the spots considered. Spot-related heatmaps characterize the expression profiles of the selected features in the series of samples. Single spot summary sheets provide detailed information on each of the spots such as the ranked list of samples which overexpress this feature in decreasing order according to the mean t-shrinkage statistics of the spot and the ranked list of the overrepresented gene sets together with the histogram of the respective p-value distribution. |
| Type | Summary Sheets | Spot's CSV tables |
|---|---|---|
| Overexpression | A B C D E F G H I J K L M N O P Q R | |
| Underexpression | a b c d e f g h i j k l m n | |
| Mutual Correlation | A B C D E F G H I J K L M N O P Q R S T U V W X Y Z A1 B1 C1 D1 | |
| k-Means Clustering | A B C D E F G H I J K L M N O P Q R S T U V W X Y | |
| Group Overexpression | A B C D E |
| Spot repots contain assignment of the spots to featuring samples and to respective sample groups. Additionally, relative numbers of significant gene sets are given for each spot and gene set category. |
| Type | Summary Sheets |
|---|---|
| Overexpression | |
| Underexpression | |
| K-Means |
| Networks of spot association are visualized as graphs. Both, correlation networks (connecting spots with r>0.5) and correlation spanning trees, are given for individual spots and also for patterns of spots occuring in the sample SOM images. |
| Type | Summary Sheets |
|---|---|
| Overexpression | |
| Underexpression | |
| K-Means |
| For each spot, enrichment of chromosomal postitions (chromosome/band) is visualized as overview heatmaps and individual chromosome plots. |
| Type | Summary Sheets |
|---|---|
| Overexpression | |
| Underexpression | |
| K-Means |