Help - Local Coherence Detection - Wodak Lab

The LCD algorithm requires inputs for several parameters from users. Default parameters are provided, but you can modify them to explore different biclusterings.

R Value Cooling rate for simulated annealing
T Value Initial temperature for simulated annealing
Min Rows Minimum number of rows for output biclusters
Min Cols Minimum number of columns for output biclusters
Number of Biclusters Number of biclusters to be initalized
Input threshold Threshold for background values
Row weight Control dimension of biclusters

Once you are satisfied with the parameters, click 'Run' to start the LCD algorithm. Once complete, a table will be generated with each row corresponding to a bicluster.

In the table, column 'biclust id' is a numeric id for biclusters, 'fitness' is the fitness score of the biclusters, 'num rows' denotes number of query genes (or size of the modules), and 'num cols' indicates number of library genes defining the bicluster. Each column can be sorted by clicking on the column headings.

Click on any row to display a heatmap showing the query genes and library genes of the selected bicluster.

Both biclusters and heatmap images can be saved locally.

Please note that this software only serves as an illustration of the LCD algorithm. Not all biclusters identified here are statistically significant. Random controls are required to establish statistical significance. It is not expected to find all significant biclusters in a single run either. Multiple random starts are required for an exhaustive analysis.

Local Coherence Detection