2D annotation enrichment
1 General =====
- Type: - Matrix Processing
- Heading: - Annot. columns
- Source code: not public.
1.1 Brief description
For every term in the categorical columns it is tested whether the corresponding expression values have a distribution in two-dimensional planes of expression values that is deviating from the global distribution. For details see Cox and Mann (2012) (Cox and Mann 2012) .
Output: The output matrix contains a list of terms from all categorical columns that are significantly biased compared to the global distribution.
2 Parameters
2.1 Columns1
Selected numerical/expression columns that are used as x-axis for the testing of the 2D distributions (default: no expression/numerical columns are selected).
Hint: The selected number of columns in “Columns1” have to be equal to the selected ones in “Columns2”.
2.2 Columns2
Selected numerical/expression columns that are used as y-axis for the testing of the 2D distributions (default: no expression/numerical columns are selected).
Hint: The selected number of columns in “Columns2” have to be equal to the selected ones in “Columns1”.
2.3 Use for truncation
The truncation can be based on p-values or the Benjamini-Hochberg correction for multiple hypothesis testing (default: Benjamini-Hochberg FDR). Rows with a test result below a specified value (“Threshold value”) are reported as significant.
2.4 Threshold value
Based on a specified threshold (default: 0.02) a row is reported as significant, if its test result is below the defined value. Depending on the chosen truncation score this threshold value is applied to the p-value or to the Benjamini-Hochberg FDR.
2.5 Relative enrichment
Selected text column, where all rows having the same identifier will be counted as one entity in the 2D annotation enrichment analysis (default: <None>). The main application is for post-translational modification sites. Then one should select here protein or gene identifiers.
This will make sure that multiple sites from the same protein (or gene) are counted only once for the enrichment analysis.
3 Parameter window
