Tool description

PANDA reconstructs a gene regulatory network using TF PPI, TF DNA binding motif, and gene expression samples. LIONESS reconstructs patient-specific PANDA networks for each gene expression sample. To download patient-specific networks, you can check the phenotypic information of the TCGA dataset. You can also select the networks by clinical variables or download all the samples in a single file.
The variable Samples indicates the number of samples used for network reconstruction. For single-sample networks, clicking the number of samples links to the phenotypic variable table and the individual networks. The number in the Sample variable and the phenotypic variable table may be different because the table can include samples from other studies. For example, in colon cancer, 444 TCGA samples were used to build LIONESS networks in a first study and 445 samples were used for a more recent study. The superset of both TCGA samples is comprised of 487 samples, which is the size of the pheotypic variables table. This discrepancy is due to different pre-processinng techniques, inclusion/exclusion criteria, and sample quality-control.