Cancer

Atlas of Cancer Signalling Network

ACSN purpose

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 Network (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. The content of the maps is curated by specialists in the corresponding fields.

ACSN features

ACSN maps are cancer-specific. ACSN aims to collect, organize and graphically represent non-disease molecular mechanisms lying behind well-defined cancer hallmarks (Hanahan and Weinberg, 2011). ACSN concentrates on exhaustive representation of molecular mechanisms that are frequently dysregulated in cancer such as cell cycle, DNA repair, cell death, survival, immune response signalling, telomere maintenance and others.

ACSN maps are interconnected. ACSN signalling maps create a geographical-like view of cancer signalling, but, unlike geography, the same molecular entity can participate in several pathways, connecting them together, and this is reflected explicitly in ACSN. 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.

ACSN maps are systematic and detailed. The maps are manually created based on the information extracted from scientific literature. Maps are constructed using the CellDesigner tool. Each map contains information about interactions between proteins, protein modifiers, post-translational modifications, protein complexes, genes, RNAs, microRNAs, small molecules and drugs. ACSN maps are reaction networks represented using process diagram description graphical language. Each map covers hundreds of molecular players and reactions; each entity on the map is annotated by references to the article and specific notes added by the map manager.

ACSN structure. ACSN is constructed as a global "geographical atlas" of cancer signalling. The atlas consists of a global "world map", maps of "continents", each representing a particular cellular function (e. g. Cell Cycle or Apoptosis). Each continent map is sub-divided into "countries" or functional modules representing signalling pathways (e.g. WNT pathway or Homologous recombination pathway).

ACSN zoom levels. 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 top-level view shows the general architecture of the atlas. The next zoom exposes locations of known oncogenes or tumor supressors. The third zoom level adds some of the most participating proteins and complexes in the atlas. Furthermore, two zooms visualize components of the atlas and reaction edges between them. Finally at the most detailed zoom level all details of maps are demonstrated including names of all entities, post-translational modifications, complexes’ names, reactions IDs and all regulators and catalyzer of reactions.

Browsing and commenting ACSN via the NaviCell tool. The ACSN map navigation, curation and maintenance are enabled by a user friendly Google Maps-based tool NaviCell. The tool is characterized by the unique combination of three essential features: (1) map navigation based on Google Maps engine, (2) semantic zooming for viewing different levels of details of the map and (3) integrated web-based blog for collecting the community curation feedback.

Visualization and analysis of 'omics data using ACSN. The visualization module is a set of functions that can be used to visualize various types of 'omics data on the ACSN molecular maps. It is available at the bottom of the right-hand panel on the ACSN maps browsing interface.

Publications

Press releases

ACSN in GARUDA Alliance

Development Team

The list of all past and present members can be found at https://acsn.curie.fr/about.html

Inna Kuperstein Inna Kuperstein, PhD
Institut Curie, Paris, France
ACSN Project Coordinator
Eric Viara Eric Viara, PhD
SYSRA, Paris, France and Institut Curie, Paris, France
Software Developer
Maria Kondratova Maria Kondratova, PhD
Institut Curie, Paris, France
Researcher
Laurence Calzone Laurence Calzone, PhD
Institut Curie, Paris, France
Senior Researcher
Loredana Martignetti Loredana Martignetti, PhD
Institut Curie, Paris, France
Senior Researcher
Urszula Czerwinska Urszula Czerwinska, MSc
Institut Curie, Paris, France
PhD Student
Jean-Marie Ravel Jean-Marie Ravel, MSc, MD
University of Pierre and Marie Curie (UPMC-Paris VI), Paris, France
Intern
Fatou Ndao Fatou Ndao, BSc
University of Bordeaux, Bordeaux, France
Intern
Alexandre Klinge Alexandre Klinge, PhD
Institut Curie, Paris, France
Scientific Coordinator of Computational Systems Biology of Cancer group
Andrei Zinovyev Andrei Zinovyev, PhD
University of Bordeaux, Bordeaux, France
Scientific Coordinator of Computational Systems Biology of Cancer group
Emmanuel Barillot Emmanuel Barillot, PhD
Institut Curie, Paris, France
Director of the U900 Institut Curie/INSERM/Ecole de Mines ParisTech

Funding