Objective
The aim of this project is to develop open source tools enabling to identify in silico potential cis-regulatory modules, as well as the transcription factors (TF) that bind to them. A publicly available genomic resource describing TF across chordate geno mes, including mammals, fish and ascidians, will be developed. Based on this resource, large-scale sequence comparisons of orthologous non-coding regions of TF genes will be performed. Moreover, a comprehensive in-vitro study of DNA-binding affinity of T F proteins will be used to build novel models of TF binding sites. Multidisciplinary approaches will be developed to identify the cis-regulatory regions driving TF gene expression. The basic steps undertaken will be: 1.Genome wide census and phylogenetic analysis of all TFs in sequenced chordate genomes. 2.Genome wide identification of Multi Species Conserved Sequences (MCSs) within orhtologous regulatory regions of chordate TFs. 3.Characterization of the activity of the identified MCSs in Ciona and zebra fish embryos, mammalian cells as well as in transgenic mice. 4.Training of a novel algorithm to predict and characterize MCSs active in various model systems 5.Comprehensive determination of the in vitro DNA-binding specificity of all transcription factor s in a chordate genome 6.Building novel bioinformatics models of TF binding sites based on complex grammars such as Hidden Markov Models and Stochastic Context Free Grammar 7.Integration of the above data into a publicly available, open source bioinformat ics tool that can be used either via the project website or downloaded for large-scale projects This project is a large-scale pluri-disciplinary effort to decipher the grammar of chordate regulatory sequences,and will have a strong impact by building too ls and resources that will enable to devise more sophisticated hypotheses regarding regulatory networks, especially those of TFs which are involved in fundamental biological processes.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences biochemistry biomolecules proteins
- social sciences sociology demography census
- natural sciences biological sciences zoology mammalogy
- medical and health sciences clinical medicine embryology
- natural sciences biological sciences genetics genomes
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Topic(s)
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
FP6-2003-LIFESCIHEALTH-I
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Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Coordinator
ROME
Italy
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.