Atlas of Cancer Signalling Network and NaviCell
There are numerous dysregulated cell signalling mechanisms in cancer. To understand involvement of and crosstalk between different mechanisms in disease initiation and development, systematic representation of processes is needed. To achieve the goal, we have initiated the construction of the Atlas of Cancer Signaling Networks (ACSN). ACSN aims to cover a majority of molecular processes implicated in cancer. ACSN signalling networks maps are manually created and annotated using systems biology standards. ACSN signalling maps create a ‘geographical-like’ view of cancer signalling. To keep track of canonically-defined pathways, signalling pathways are indicated on the maps as functional modules and can be visualized in the context of the whole network or as separate maps. The atlas can be view at several zoom levels. To facilitate the exploration, each level of zoom on the atlas exposes a certain depth of detail. The most detailed zoom level all details of maps are demonstrated including regulators and catalyzer of reactions. The visualization module is a set of functions that can be used to visualize various types of omics and clinical data on the ACSN molecular maps, allowing interpretation of the cancer data and stratification of patients according to their network-based molecular signatures.
Application of Atlas of Cancer Signalling Network in preclinical studies, Briefings in Bioinformatics, Volume 20, Issue 2, March 2019, Pages 701–716, https://doi.org/10.1093/bib/bby031
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. Oncogenesis 4, e160 (2015). https://doi.org/10.1038/oncsis.2015.19
NaviCell: a web tool for exploring large maps of molecular interactions
NaviCell platform provides an easy map navigation and its annotations using Google maps™ engine. The logic of navigation as scrolling and zooming; features as markers, pop-up bubbles and zoom bar are adapted from the Google map. NaviCell semantic zooming provides possibility for map exploring from detailed toward a top-level view achieved by gradual exclusion of details while zooming out. In addition, NaviCell now includes a powerful module for data visualization. Users can map and visualize different types of "omics" data on the NaviCell maps. There is also a Python API to automate tasks and communicate with the NaviCell web server.
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst Biol 7, 100 (2013). https://doi.org/10.1186/1752-0509-7-100
NaviCell Web Service for network-based data visualization, Nucleic Acids Research, Volume 43, Issue W1, 1 July 2015, Pages W560–W565, https://doi.org/10.1093/nar/gkv450