Power laws, scale-free networks and genome biology:
Gespeichert in:
| Weitere Verfasser: | , , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2006
|
| Schriftenreihe: | Molecular Biology Intelligence Unit
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | 257 S. Ill., graph. Darst. |
| ISBN: | 0387258833 |
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| adam_text | I = CONTENTS =r
Preface xiii
1. Power Laws in Biological Networks 1
EivindAlmaas and Albert-LdszU Barabdsi
Power Laws in Network Topology 2
Network Models 3
Power Laws in Network Utilization 6
2. Graphical Analysis of Biocomplex Networks
and Transport Phenomena 12
Kwang-Il Gob, Byungnam Kahng and Doochul Kim
The Degree Distribution, the Degree Correlation
Function and the Clustering Coefficient 13
Graph Theoretic Analysis of the Yeast Protein
Interaction Network 14
Classification of Scale-Free Networks 16
3. Large-Scale Topological Properties of Molecular Networks 25
Sergei Maslov and Kim Sneppen
Topological Properties of Protein Networks 26
Multi-Node Properties: Correlation Profile 33
Robustness of the Correlation Profile with Respect
to Potential Errors in the Data 36
Discussion: What It May All Mean? 37
4. The Connectivity of Large Genetic Networks:
Design, History, or Mere Chemistry? 40
Andreas Wagner
Metabolic Networks and Planetary Atmospheres 42
Protein Interaction Networks 44
Connectivity and Protein Age 46
5. The Drosophila Protein Interaction Network
May Be neither Power-Law nor Scale-Free 53
J.S. Bader
Observed Vertex Degree Distribution 55
Vertex Degree Distributions and Power-Law Fits 56
Bait and Prey Distributions Reconciled 58
Determining the Length Scale of the Network 59
6. Birth and Death Models of Genome Evolution 65
Georgy P. Karev, Yuri I. Wolf and Eugene V. Koonin
Power Laws, Scale-Free Networks, and Models
of Genome Evolution 65
Definitions, Assumptions and Empirical Data 67
Asymptotic Behaviors of the Ergodic Distribution
of the Model 69
Linear Stochastic BDIM and Its Applications 71
Nonlinear Modifications of the Model: Polynomial BDIM 73
Nonlinear Rational BDIM 75
Simulation of Gene Family Evolution under BDIMs
of Different Degrees 79
The Mean Number of Elementary Events before Family
Extinction and Formation 79
7. Scale-Free Evolution: From Proteins to Organisms 86
Nikolay V. Dokholyan and Eugene I. Shakhnovich
Protein Evolutionary Relationships
from Structure Similarities 88
Protein Structure-Function Relations
from an Evolutionary Perspective 89
Protein Evolutionary Relations within
and between Individual Proteomes 89
Sequence Divergence 90
Why It May Be Impossible to Reconstruct Hereditary
Relations between Proteins Based Solely
on Their Sequence Similarity? 91
The Underlying Scenario of Protein Evolution 92
Reconstructing Evolutionary Relations between Proteins 93
Properties of the Protein Domain Universe Graphs 94
Evolution of Proteins and Organisms 97
Reconstruction of Protein Structure-Function Relations 98
The Importance of Independent Functional
Hierarchical Description 99
Divergent Evolution Observed 100
8. Gene Regulatory Networks 106
T. Gregory Dewey andDavidJ. Galas
Inferring Gene Expression Networks
from Microarray Data 107
Global Properties of Gene Expression Networks Ill
Gene Duplication Model of Expression Networks 113
Transcription Factor Networks 115
9. Power Law Correlations in DNA Sequences 123
Sergey V. Buldyrev
Critical Phenomena and Long Range Correlations 124
One-Dimensional Ising Model 125
Markovian Processes 126
Exponential versus Power Law Correlations 128
Correlation Analysis of DNA Sequences 131
Correlation Function 132
Fourier Power Spectrum 136
Discrete Fourier Transform 137
Detrended Fluctuation Analysis (DFA) 140
A Relation between DFA and Power Spectrum 141
Duplication-Mutation Model of DNA Evolution 144
Alternation of Nudeotide Frequencies 145
Models of Long Range Anti-Correlations 149
Analysis of DNA Sequences 151
Distribution of Simple Repeats 154
10. Analytical Evolutionary Model for Protein Fold Occurrence
in Genomes, Accounting for the Effects of Gene Duplication,
Deletion, Acquisition and Selective Pressure 165
Michael Kamak Nicholas M. Luscombe, Jiang Qian
and Mark Gerstein
Minimal Model: Gene Duplication and New Fold Acquisition 167
Extended Model: Including the Effects of Random
Gene Deletion 170
The Effects of Selection Pressure 174
Fitting the Models to Genomic Data 176
Appendix A: Analytic Solution of the Minimal Model 180
Appendix B: Crossover Behavior 182
Appendix C: Arbitrary Initial Distribution 184
Appendix D: Solution to the Extended Model
WhenO Q 1 and R = 0 184
Appendix E: Analytical Results for Higher Moments 185
Appendix F: Perturbation Theory Approximation
for the Extended Model 186
Appendix G: The Effects of Selection Pressure 189
Appendix H: A Useful Normalization Identity 192
11. The Protein Universes: Some Informatic Issues
in Protein Classification 194
5. Rackovsky
General Methodology 195
Protein Sequences 196
Protein Structures 198
12. The Role of Computation in Complex Regulatory Networks 206
Pau Femdndez and Ricard V. Soli
The Evidence for Computing Networks 208
Modeling 209
Irreducibility 211
The Boolean Idealization 212
The Evolutionary Point of View 216
Redundancy 218
Degeneracy 219
Evolvability 220
Modularity 221
13. Neutrality and Selection in the Evolution of Gene Families 226
Itai Yanai
Gene Family Sizes (GFS) Distributions 226
Modeling Genome Evolution 227
Comparative Deconstruction of the Gene Family
Sizes Distribution 228
Pleiotropy — Duplication — Subfunctionalization 232
14. Scaling Laws in the Functional Content of Genomes:
Fundamental Constants of Evolution? 236
Erik van Nimwegen
Power Laws in Genomic Quantities 236
Comparing Genomic Features across Genomes 236
Scaling in Functional Gene-Content Statistics 237
Principle Component Analysis 243
Evolutionary Interpretation 247
Methods 251
Index 255
|
| adam_txt |
I = CONTENTS =r
Preface xiii
1. Power Laws in Biological Networks 1
EivindAlmaas and Albert-LdszU Barabdsi
Power Laws in Network Topology 2
Network Models 3
Power Laws in Network Utilization 6
2. Graphical Analysis of Biocomplex Networks
and Transport Phenomena 12
Kwang-Il Gob, Byungnam Kahng and Doochul Kim
The Degree Distribution, the Degree Correlation
Function and the Clustering Coefficient 13
Graph Theoretic Analysis of the Yeast Protein
Interaction Network 14
Classification of Scale-Free Networks 16
3. Large-Scale Topological Properties of Molecular Networks 25
Sergei Maslov and Kim Sneppen
Topological Properties of Protein Networks 26
Multi-Node Properties: Correlation Profile 33
Robustness of the Correlation Profile with Respect
to Potential Errors in the Data 36
Discussion: What It May All Mean? 37
4. The Connectivity of Large Genetic Networks:
Design, History, or Mere Chemistry? 40
Andreas Wagner
Metabolic Networks and Planetary Atmospheres 42
Protein Interaction Networks 44
Connectivity and Protein Age 46
5. The Drosophila Protein Interaction Network
May Be neither Power-Law nor Scale-Free 53
J.S. Bader
Observed Vertex Degree Distribution 55
Vertex Degree Distributions and Power-Law Fits 56
Bait and Prey Distributions Reconciled 58
Determining the Length Scale of the Network 59
6. Birth and Death Models of Genome Evolution 65
Georgy P. Karev, Yuri I. Wolf and Eugene V. Koonin
Power Laws, Scale-Free Networks, and Models
of Genome Evolution 65
Definitions, Assumptions and Empirical Data 67
Asymptotic Behaviors of the Ergodic Distribution
of the Model 69
Linear Stochastic BDIM and Its Applications 71
Nonlinear Modifications of the Model: Polynomial BDIM 73
Nonlinear Rational BDIM 75
Simulation of Gene Family Evolution under BDIMs
of Different Degrees 79
The Mean Number of Elementary Events before Family
Extinction and Formation 79
7. Scale-Free Evolution: From Proteins to Organisms 86
Nikolay V. Dokholyan and Eugene I. Shakhnovich
Protein Evolutionary Relationships
from Structure Similarities 88
Protein Structure-Function Relations
from an Evolutionary Perspective 89
Protein Evolutionary Relations within
and between Individual Proteomes 89
Sequence Divergence 90
Why It May Be Impossible to Reconstruct Hereditary
Relations between Proteins Based Solely
on Their Sequence Similarity? 91
The Underlying Scenario of Protein Evolution 92
Reconstructing Evolutionary Relations between Proteins 93
Properties of the Protein Domain Universe Graphs 94
Evolution of Proteins and Organisms 97
Reconstruction of Protein Structure-Function Relations 98
The Importance of Independent Functional
Hierarchical Description 99
Divergent Evolution Observed 100
8. Gene Regulatory Networks 106
T. Gregory Dewey andDavidJ. Galas
Inferring Gene Expression Networks
from Microarray Data 107
Global Properties of Gene Expression Networks Ill
Gene Duplication Model of Expression Networks 113
Transcription Factor Networks 115
9. Power Law Correlations in DNA Sequences 123
Sergey V. Buldyrev
Critical Phenomena and Long Range Correlations 124
One-Dimensional Ising Model 125
Markovian Processes 126
Exponential versus Power Law Correlations 128
Correlation Analysis of DNA Sequences 131
Correlation Function 132
Fourier Power Spectrum 136
Discrete Fourier Transform 137
Detrended Fluctuation Analysis (DFA) 140
A Relation between DFA and Power Spectrum 141
Duplication-Mutation Model of DNA Evolution 144
Alternation of Nudeotide Frequencies 145
Models of Long Range Anti-Correlations 149
Analysis of DNA Sequences 151
Distribution of Simple Repeats 154
10. Analytical Evolutionary Model for Protein Fold Occurrence
in Genomes, Accounting for the Effects of Gene Duplication,
Deletion, Acquisition and Selective Pressure 165
Michael Kamak Nicholas M. Luscombe, Jiang Qian
and Mark Gerstein
Minimal Model: Gene Duplication and New Fold Acquisition 167
Extended Model: Including the Effects of Random
Gene Deletion 170
The Effects of Selection Pressure 174
Fitting the Models to Genomic Data 176
Appendix A: Analytic Solution of the Minimal Model 180
Appendix B: Crossover Behavior 182
Appendix C: Arbitrary Initial Distribution 184
Appendix D: Solution to the Extended Model
WhenO Q 1 and R = 0 184
Appendix E: Analytical Results for Higher Moments 185
Appendix F: Perturbation Theory Approximation
for the Extended Model 186
Appendix G: The Effects of Selection Pressure 189
Appendix H: A Useful Normalization Identity 192
11. The Protein Universes: Some Informatic Issues
in Protein Classification 194
5. Rackovsky
General Methodology 195
Protein Sequences 196
Protein Structures 198
12. The Role of Computation in Complex Regulatory Networks 206
Pau Femdndez and Ricard V. Soli
The Evidence for Computing Networks 208
Modeling 209
Irreducibility 211
The Boolean Idealization 212
The Evolutionary Point of View 216
Redundancy 218
Degeneracy 219
Evolvability 220
Modularity 221
13. Neutrality and Selection in the Evolution of Gene Families 226
Itai Yanai
Gene Family Sizes (GFS) Distributions 226
Modeling Genome Evolution 227
Comparative Deconstruction of the Gene Family
Sizes Distribution 228
Pleiotropy — Duplication — Subfunctionalization 232
14. Scaling Laws in the Functional Content of Genomes:
Fundamental Constants of Evolution? 236
Erik van Nimwegen
Power Laws in Genomic Quantities 236
Comparing Genomic Features across Genomes 236
Scaling in Functional Gene-Content Statistics 237
Principle Component Analysis 243
Evolutionary Interpretation 247
Methods 251
Index 255 |
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| spelling | Power laws, scale-free networks and genome biology Eugene V. Koonin ; Georgy Karev ; Yuri Wolf (eds.) Berlin [u.a.] Springer 2006 257 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Molecular Biology Intelligence Unit Molekulargenetik (DE-588)4039987-4 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Biomathematik (DE-588)4139408-2 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Molekularbiologie (DE-588)4039983-7 s Biomathematik (DE-588)4139408-2 s DE-604 Molekulargenetik (DE-588)4039987-4 s b DE-604 Koonin, Eugene V. (DE-588)136629008 edt Karev, Georgij P. edt Wolf, Yuri edt text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2739540&prov=M&dok_var=1&dok_ext=htm Inhaltstext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014633839&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Power laws, scale-free networks and genome biology Molekulargenetik (DE-588)4039987-4 gnd Molekularbiologie (DE-588)4039983-7 gnd Biomathematik (DE-588)4139408-2 gnd |
| subject_GND | (DE-588)4039987-4 (DE-588)4039983-7 (DE-588)4139408-2 (DE-588)4143413-4 |
| title | Power laws, scale-free networks and genome biology |
| title_auth | Power laws, scale-free networks and genome biology |
| title_exact_search | Power laws, scale-free networks and genome biology |
| title_exact_search_txtP | Power laws, scale-free networks and genome biology |
| title_full | Power laws, scale-free networks and genome biology Eugene V. Koonin ; Georgy Karev ; Yuri Wolf (eds.) |
| title_fullStr | Power laws, scale-free networks and genome biology Eugene V. Koonin ; Georgy Karev ; Yuri Wolf (eds.) |
| title_full_unstemmed | Power laws, scale-free networks and genome biology Eugene V. Koonin ; Georgy Karev ; Yuri Wolf (eds.) |
| title_short | Power laws, scale-free networks and genome biology |
| title_sort | power laws scale free networks and genome biology |
| topic | Molekulargenetik (DE-588)4039987-4 gnd Molekularbiologie (DE-588)4039983-7 gnd Biomathematik (DE-588)4139408-2 gnd |
| topic_facet | Molekulargenetik Molekularbiologie Biomathematik Aufsatzsammlung |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=2739540&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014633839&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT koonineugenev powerlawsscalefreenetworksandgenomebiology AT karevgeorgijp powerlawsscalefreenetworksandgenomebiology AT wolfyuri powerlawsscalefreenetworksandgenomebiology |