ACSN (https://acsn.curie.fr) is a web-based multi-scale resource of biological maps depicting molecular processes in cancer cell and tumor microenvironment. The Atlas represents interconnected cancer-related signalling and metabolic network maps. Molecular mechanisms are depicted on the maps at the level of biochemical interactions, forming a large seamless network of above 8000 reactions covering close to 3000 proteins and 800 genes and based on more than 4500 scientific publications. The Atlas is a "geographic-like" interactive "world map" of molecular interactions leading the hallmarks of cancer as described by Hanahan and Weinberg. Read more|Hide
Molecular mechanisms within cancer cell and components of tumor microenvironment are represented in the form of comprehensive maps manually created using systems biology standards, making these maps amenable for computational analysis. The content of the maps reflects the most recent knowledge on mechanisms implicated in cancer development.
The maps of ACSN 2.0 (https://acsn.curie.fr/Temp/maps.html) are interconnected, the regulatory loops between cancer cell and tumor microenvironment are systematically depicted. The cross-talk between signalling mechanisms and metabolic processes in the cancer cells is explicitly depicted thanks to new feature of the Atlas: ACSN 2.0 is now connected to RECON metabolic network, the largest graphical representation of human metabolism.
ACSN 2.0 is composed of 13 maps, which are all interconnected. There are six maps covering signalling processes involved in cancer cell development and four maps describing tumor microenvironment. In addition, there are 3 cell type-specific maps describing specific signalling within different cells types found in the surrounding mullei of cancer cell. This feature of ACSN 2.0 reflects heterogeneity of tumor microenvironment.
The maps of ACSN 2.0 have an hierarchical structure. They are decomposed into functional modules with understandable network layout. Navigation of the ACSN 2.0 is intuitive thanks to Google Maps-like features of NaviCell web platform. The exploration of the Atlas is simplified due to the semantic zooming feature, allowing to explore the seamless Atlas and individual maps from ACSN 2.0 collection at different levels of details description.
Cross-referencing with other databases and links to all scientific paper that were used for composition of the Atlas, allow the user to study in depth the features of ACSN 2.0 components.
The ACSN content is permanently expanded with new signalling network maps and updated by the latest discoveries in the field of cancer-related cell signalling. In addition, ACSN is not only a cancer-oriented database: ACSN maps depict fundamental cell signalling processes and can be used in cell signalling research.
The integrated NaviCell web-based tool box in the ACSN 2.0 resource, allows to import and visualize heterogeneous omics data on top of the ACSN 2.0 maps and to perform functional analysis of the maps. In addition, the associated NaviCom tool automatically generates ACSN-based molecular portraits of cancer using multi-level omics data from cancer data resources as cBioPortal.
By using the Atlas (through the web interface, or the files you can download), you agree to cite it in any communication by refering to our main paper:
Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. Oncogenesis. 2015 Jul 20;4:e160. doi: 10.1038/oncsis.2015.19. Pubmed ID: 26192618.
ACSN 2.0 in Numbers
|Maps||Species||Proteins||RNAs||Antisense RNAs||Genes||Simple Molecules||Small Molecules||Reactions||References|
|ACSN 2.0 Resource||9692||2997||740||130||808||665||775||8137||4532|
|Cancer Cell Map||7024||2329||531||120||593||492||596||5955||3121|
|Cell cycle and DNA repair Map||723||277||17||0||87||10||14||544||646|
|Cell Survival Map||1967||580||106||25||123||121||149||1341||869|
|Regulated Cell Death Map||2659||1008||260||93||215||338||407||2020||855|
|Telomere Maintenance Map||153||93||3||0||14||11||11||105||70|
|Invasion and Motility Map||390||117||41||6||49||25||35||364||63|
|Tumor Microenvironment Map||2844||949||253||32||261||204||211||2182||1441|
|Adaptive Immunity Map||492||281||42||0||29||38||42||338||417|
|Innate Immunity Map||1466||583||152||20||165||104||108||1084||836|
|CAF Cell Map||682||300||86||13||87||41||41||581||380|
|Natural Killer Cell map||567||249||42||14||53||25||29||377||336|
|Macrophages and MDSC Cells map||588||217||95||4||95||42||44||457||214|
|Dendritic Cell map||491||226||44||1||43||38||40||346||333|
The maps on ACSN 2.0 are based on literature extracted from specialized journals.
Due to its uniqueness, ACSN 2.0 has a large number of unique references.
ACSN 2.0 References are quite recent, making it an up-to-date resource.
Tools related to ACSN 2.0
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 feedbacks
NaviCom is a platform for generating interactive network based molecular portraits using high-throughput datasets. It connects the cBioPortal database and NaviCell web service and allows to display various high-throughput data types simultaneously on the network maps in one click.
ACSN is part of the Disease Maps Project, an open community effort to comprehensively represent disease mechanisms for various diseases.
ACSN has been mentioned in many publications, find some here:
L Cristobal Monraz Gomez, Maria Kondratova, Jean-Marie Ravel, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein; Application of Atlas of Cancer Signalling Network in preclinical studies, Briefings in Bioinformatics, bby031, https://doi.org/10.1093/bib/bby031.
Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein; Signalling maps in cancer research: construction and data analysis, Database, Volume 2018, 1 January 2018, bay036, https://doi.org/10.1093/database/bay036.
Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Zinovyev; 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
Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein; NaviCom: a web application to create interactive molecular network portraits using multi-level omics data, Database, Volume 2017, 1 January 2017, bax026, https://doi.org/10.1093/database/bax026
Wael Jdey, Sylvain Thierry, Christophe Russo, et al; Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors ,Clin Cancer Res February 15 2017 (23) (4) 1001-1011; DOI: 10.1158/1078-0432.CCR-16-1193
Lonjou, Christine, et al; Investigation of DNA repair-related SNPs underlying susceptibility to papillary thyroid carcinoma reveals MGMT as a novel candidate gene in Belarusian children exposed to radiation. BMC cancer 17.1 (2017): 328; DOI: 10.1186/s12885-017-3314-5
Kuperstein I, Robine S, Zinovyev A; Network biology elucidates metastatic colon cancer mechanisms. 2015. Cell Cycle 14(14):2189-90. DOI: 10.1080/15384101.2015.1060816.
Costa, Ana et al; Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer. Cancer Cell , Volume 33 , Issue 3 , 463 - 479.e10. DOI: 10.1016/j.ccell.2018.01.011.
ACSN 2.0 team
ACSN resource is developed at Institut Curie by the Computational Systems Biology of Cancer team
Cristobal Monraz Gomez
Hien Anh Nguyen
ACSN former members
Hien Anh Nguyen
ACSN 2.0 contributors
- Sebastian D Amigorena, Institut Curie, PSL Research University, Inserm, U932, F-75005, Paris, FranceDenis Thieffry, Ecole Normale Supérieure - Département de Biologie, IBENS - UMR ENS - CNRS 8197 - INSERM 1024, Paris France.
- Mathieu Boissan, Centre de recherche St-Antoine, Inserm, UMR938, Sorbonne Université, Paris, FranceGordon Tucker, Oncology Research and Development Unit, Institut de Recherches SERVIER, Croissy-sur-Seine, France.
- Guido Kroemer, UMR1138, Centre de Recherche des Cordeliers, Paris, France
- Jennifer Modamio, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Eschsur-Alzette, L-4362, LuxembourgPhilippe Chavrier, Institut Curie, Membrane and Cytoskeleton Dynamics, CNRS UMR 144, Paris, France.
- Vassili Soumelis, Institut Curie, PSL Research University, Inserm, U932, F-75005, Paris, France
- Ines Thiele, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Eschsur-Alzette, L-4362, Luxembourg
- Ronan M. T. Fleming, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden, Leiden, 2333, The Netherlands