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QUANTITATIVE LAWS, Week 2
Scaling laws in the bacterial genomic
repertoires.
Eleonora De Lazzari
Université Pierre-et-Mari...
Genomic repertoires as modular systems
Functional categories
Evolutionary categories
(domain-families)
Genome
components
r...
Scaling Laws in Genomics
Functional
categories
Evolutionary
categories
~ 1000 bacterial
genomes
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
Translati...
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
Translati...
Do domain-families have scaling laws?
functional category (Transferases)
βC = 1
TK C-terminal domain-like Acyl-CoA N-acylt...
How do family-scalings sum?
Few highly populated families determine
the scaling of the whole TF category.
Transcription
Fa...
To what extent a range of family exponents is
peculiar to a functional category?
Method:
Grouping families with
similar ex...
To what extent a range of family exponents is
peculiar to a functional category?
Grouping families with
similar exp. shows...
To what extent a range of family exponents is
peculiar to a functional category?
Grouping families with
similar exp. shows...
Marco Cosentino Lagomarsino
CNRS, UMR 7238, Paris, France
Jacopo Grilli
Department of Ecology and Evolution, University of...
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Scaling laws in the bacterial genomic repertoires - Eleonora De Lazzari

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QUANTITATIVE LAWS June 13 -June 24

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Scaling laws in the bacterial genomic repertoires - Eleonora De Lazzari

  1. 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. 2. Genomic repertoires as modular systems Functional categories Evolutionary categories (domain-families) Genome components realization
  3. 3. Scaling Laws in Genomics Functional categories Evolutionary categories ~ 1000 bacterial genomes
  4. 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. 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. 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. 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. 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. 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. 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. 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 !

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