There are several classes of output from Multi-Dendrix. This page will explain each of the files, and give an overview of the file formats.
The collections of pathways identified by Multi-Dendrix are stored as individual, tab-separated text files. The files represent tables in the following format:
| Weight | Direct interactions statistic (optional) | Direct interactions P-value (optional) | Genes |
| 61 | 2 | 0.0 | CDKN2B, CDK4, RB1 |
| 57 | 1 | 0.0 | CDKN2A, TP53, DTX3 |
The analysis of subtype-specific mutations is output in a tab-separated table of the following format:
| Gene | (Sub)-type | Type Mutations | Type Normal | Non-Type Mutations | Non-Type Normal | P-Value | Bonferonni- Corrected P-Value |
| TP53 | Basal-like | 74 | 24 | 112 | 313 | 2.55E-19 | 1.53E-18 |
Output from the permute_mutation_data module. Same output format as the input mutation data format (see Input File Formats).
Output from the permute_ppi_network module. Same output format as the input PPI network format (see Input File Formats).