Cystic fibrosis

Cystic Fibrosis Map (CyFi-MAP)

The Cystic Fibrosis Map project (CyFi-MAP) is an effort focused on high-quality description of cystic fibrosis mechanisms and building a predictive computational model based on this description.

The map of cystic fibrosis mechanisms

The following approach is used to develop a map of the cystic fibrosis mechanisms. Information from literature is integrated into a large-scale Activity Flow diagram. Particular focus is on various types of mutations of CFTR gene. Information from pathway databases, for example Reactome and PANTHER, is reused when possible, and contextualised. The network is presented in the Systems Biology Graphical Notation standard (Le Novère, 2009, doi:10.1038/nbt.1558). A community of domain experts is involved to ensure that the disease mechanisms are adequately represented.

The model of cystic fibrosis

The goal of the project is to develop a computational model of molecular mechanisms which are affected in cystic fibrosis and to quantitatively elucidate the underlying molecular and cellular events. A computational model of cystic fibrosis is based on the CF-MAP reconstruction. Hypothesis and assumptions are added on the top of the known described mechanisms.

The objectives are:

1. Integrate the published ‘omics data for a broader view of CF allowing for an integrated perspective of the available knowledge which will include the relevant molecular interactions. This will involve bringing together the available data in a flexible information system that is able to encompass the relevant information and metadata.

2. Construct a logical model network from the available data using Bayesian or Markov model.

3. Test and stress the developed model so that it is possible to make an inference by changing and modifying the model inputs. Results will be verified against available experimental data and new experiments will be proposed to validate the model consistency.

Resources dedicated

The project was initiated by the University of Lisbon and is designed as a joint effort of experts in cystic fibrosis and computational biology research groups. It progresses in the format of a PhD project and is led by Catarina Pereira, a PhD student at the University of Lisbon.

We welcome collaboration and would be happy to join efforts with similar projects.

CF-MAP Development Team

	Catarina Pereira, MSc University of Lisbon, Portugal PhD Student, Leader of the CyFi-MAP project
	André Falcão, PhD University of Lisbon, Portugal Assistant Professor, Department of Informatics, Faculty of Sciences Supervisor of the CyFi-MAP PhD project
	Margarida D. Amaral, PhD University of Lisbon, Portugal Professor, Chemistry and Biochemistry Department, Faculty of Sciences Co-supervisor of the CyFi-MAP PhD project
	Alexander Mazein, PhD Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg Researcher Co-supervisor of the CyFi-MAP PhD project

CyFi-MAP Editorial Panel

The list of domain experts is being confirmed.

Contact

To contribute and discuss the project please use this email address: cysticfibrosismap@googlegroups.com

Project Leader:
Catarina Pereira cpereira@lasige.di.fc.ul.pt

Funding

This work is supported by the Fundação para a Ciência e a Tecnologia through the PhD Grant ref. PD/BD/131405/2017.