The paad.cregmap user interface includes three main tabs: “CoRegNet”, “CoRegMap” and “Add new data”:

  1. With the 'CoRegNet' tab, the coregulatory network inferred from the transcriptome of cancer-derived cell lines is visualized. CoRegNet network representations are intuitively understandable and facilitate the integration of several layers of information over nodes and edges. Nodes represent transcription factors and cofactors (TFs/coTFs). Node color (red= high; blue = low) indicates the influence of the corresponding TF/coTF. Node size is proportional to the number of targets of the TF/coTF and the intensity of the color indicates the strength of its influence. The coregulatory interactions between nodes are indicated as follows: predicted co-operativity interactions are shown in gray, and interactions for which there is published evidence are shown in blue (for protein-protein interactions, ppi) or red (for transcriptional regulation, tfbs). This tab is designed to allow users to explore the coregulatory network and to identify core active coregulators in single sample (e.g., cell line) or particular phenotype (e.g., tumor subtype) for further analysis.


  2. The "CoRegMap" tab displays an interactive uniform manifold approximation and projection (UMAP) plot of the regulatory influence signal matrix of large tumor metacohort database. The "CoRegMap" tab also allows users 1) to annotate samples with several items of information, including molecular subtype, influence of the regulator, copy number variation, somatic mutations, clinical data and a CRISPR/Cas9 screen-based DepMap gene essentiality score for the survival/proliferation of cell lines. 2) to align (comparability of transcriptional profiles) tumors and patient-derived cell lines, xenografts and/or organoid models.


  3. Finally, and most importantly, query datasets can be mapped to paad.cregmap with the “add new data” tab. paad.cregmap allow users with no programming skills to upload their expression datasets or to retrieve expression datasets from Gene Expression Omnibus (GEO). PAAD-cRegMap calculates, in a few seconds, the influence of coregulators for the new data, displaying the results in the references compounds (CoRegNet and CoRegMap).