Scaling laws in the bacterial genomic repertoires - Eleonora De Lazzari
•
0 j'aime•547 vues
QUANTITATIVE LAWS June 13 -June 24
Recommandé
Contenu connexe
Tendances
Tendances (13)
Similaire à Scaling laws in the bacterial genomic repertoires - Eleonora De Lazzari
Similaire à Scaling laws in the bacterial genomic repertoires - Eleonora De Lazzari (20)
Plus de Lake Como School of Advanced Studies
Plus de Lake Como School of Advanced Studies (20)
Dernier
Dernier (20)
Scaling laws in the bacterial genomic repertoires - Eleonora De Lazzari
- 1. QUANTITATIVE LAWS, Week 2 Scaling laws in the bacterial genomic repertoires. Eleonora De Lazzari Université Pierre-et-Marie-Curie - Laboratory of Computational and Quantitative Biology
- 2. Genomic repertoires as modular systems Functional categories Evolutionary categories (domain-families) Genome components realization
- 3. Scaling Laws in Genomics Functional categories Evolutionary categories ~ 1000 bacterial genomes
- 4. Scaling Laws in Genomics nC ~ nβC βMET ~ 1 βTF ~ 2 βTRANSL ~ const. 10 3 10 410 0 10 1 10 2 10 3 10 4 Metabolism Translation Transcr. regulation FunctionalCategorySize(nC) Genome Size (n) [VanNimwegen 2003, TRENDS in Genetics] Functional categories Evolutionary categories ~ 1000 bacterial genomes components = size = #domains
- 5. Scaling Laws in Genomics nC ~ nβC βMET ~ 1 βTF ~ 2 βTRANSL ~ const. 10 3 10 410 0 10 1 10 2 10 3 10 4 Metabolism Translation Transcr. regulation FunctionalCategorySize(nC) Genome Size (n) [VanNimwegen 2003, TRENDS in Genetics] Functional categories Evolutionary categories ~ 1000 bacterial genomes components = How does the abundance of genes performing specific functions emerge from evolutionary moves at the family level?
- 6. Do domain-families have scaling laws? functional category (Transferases) βC = 1 TK C-terminal domain-like Acyl-CoA N-acyltransferases 10 3 10 4 10 0 10 1 10 2 familysize(ni) genome size (n) β = 0.6 genome size (n) familysize(ni) 10 3 10 4 10 0 10 1 10 2 β = 1.6 yes, but often different from the category! size = # domains
- 7. How do family-scalings sum? Few highly populated families determine the scaling of the whole TF category. Transcription Factors 2.5 1.5 0.5 -0.5 0 5 10 15 20 25 30 Exponent Rank in domain abundance 5th biggest family funcional cat. without the first 5 families
- 8. To what extent a range of family exponents is peculiar to a functional category? Method: Grouping families with similar exp. shows known associations and reveal new one: 0.0 0.8 1.6 0.0 0.5 1.0 1.5 2.0 protein modification transferases signal transduction DNA-binding translation β* category exp βC families with similar exp: [β*-δ, β*+δ] over-represented ∩ Zscore > 2 under-represented Zscore < 2 Functional category βC β*
- 9. To what extent a range of family exponents is peculiar to a functional category? Grouping families with similar exp. shows known associations and reveal new one: 0.0 0.8 1.6 0.0 0.5 1.0 1.5 2.0 protein modification transferases signal transduction DNA-binding translation β* category exp βC Exponent Rank in domain abundance ATPase domain of HSP90 chaperone / DNA topoisomerase II / histidine kinase 0 10 15 0 1 2
- 10. To what extent a range of family exponents is peculiar to a functional category? Grouping families with similar exp. shows known associations and reveal new one: 0.0 0.8 1.6 0.0 0.5 1.0 1.5 2.0 protein modification transferases signal transduction DNA-binding translation β* category exp βC unknown function nucleotide metabolism and transport Other outliers:
- 11. Marco Cosentino Lagomarsino CNRS, UMR 7238, Paris, France Jacopo Grilli Department of Ecology and Evolution, University of Chicago, 1101 E 57th st 60637 Chicago, IL Sergei Maslov Bioengineering Department, University of Illinois at Urbana- Champaign, Urbana, IL 61801 Thank you !