scaling laws in the bacterial genomic repertoires - eleonora de lazzari
TRANSCRIPT
QUANTITATIVE LAWS, Week 2
Scaling laws in the bacterial genomic repertoires.
Eleonora De LazzariUniversité Pierre-et-Marie-Curie - Laboratory of Computational and Quantitative Biology
Genomic repertoires as modular systems
Functional categories
Evolutionary categories(domain-families)
Genome
components
realization
Scaling Laws in Genomics
Functional categories
Evolutionary categories
~ 1000 bacterial genomes
Scaling Laws in Genomics
nC ~ nβC
βMET ~ 1
βTF ~ 2
βTRANSL ~ const.
103 104100
101
102
103
104
Metabolism
Translation
Transcr. regulation
Fun
ctio
nal C
ateg
ory
Siz
e (n
C)
Genome Size (n)
[VanNimwegen 2003, TRENDS in Genetics]
Functional categories
Evolutionary categories
~ 1000 bacterial genomes
components =
size = #domains
Scaling Laws in Genomics
nC ~ nβC
βMET ~ 1
βTF ~ 2
βTRANSL ~ const.
103 104100
101
102
103
104
Metabolism
Translation
Transcr. regulation
Fun
ctio
nal C
ateg
ory
Siz
e (n
C)
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?
Do domain-families have scaling laws?
functional category (Transferases)βC = 1
TK C-terminal domain-like Acyl-CoA N-acyltransferases
103 104100
101
102
fam
ily s
ize
(ni)
genome size (n)
β = 0.6
genome size (n)fa
mily
siz
e (n
i)
103 104100
101
102
β = 1.6
yes, but often different from the category!
size = # domains
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
Exp
onen
t
Rank in domain abundance
5th biggest familyfuncional cat. without the first 5 families
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 1.60.0
0.5
1.0
1.5
2.0protein 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 categoryβC
β*
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 1.60.0
0.5
1.0
1.5
2.0protein modification
transferases
signal transduction
DNA-binding
translation
β*
category exp βC
Exp
onen
t
Rank in domain abundance
ATPase domain of HSP90 chaperone / DNA topoisomerase II / histidine kinase
0 10 15
0
1
2
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 1.60.0
0.5
1.0
1.5
2.0protein modification
transferases
signal transduction
DNA-binding
translation
β*
category exp βC
unknown function
nucleotide metabolism and transport
Other outliers:
Marco Cosentino LagomarsinoCNRS, UMR 7238, Paris, France
Jacopo GrilliDepartment of Ecology and Evolution, University of Chicago, 1101 E 57th st 60637 Chicago, IL
Sergei MaslovBioengineering Department, University of Illinois at Urbana-Champaign, Urbana, IL 61801
Thank you !