Not all scale free networks are born equal: The role of the seed graph in PPI network emulation

Fereydoun Hormozdiari, Petra Berenbrink, Nataša Pržulj, Cenk Sahinalp

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The (asymptotic) degree distributions of the best known "scale free" network models are all similar and are independent of the seed graph used. Hence it has been tempting to assume that networks generated by these models are similar in general. In this paper we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the "right" seed graph, the duplication model captures many topological features of publicly available PPI networks very well.

Original languageEnglish (US)
Title of host publicationSystems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers
Pages1-13
Number of pages13
StatePublished - Dec 1 2007
Externally publishedYes
EventJoint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics - San Diego, CA, United States
Duration: Dec 1 2006Dec 3 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4532 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

OtherJoint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics
CountryUnited States
CitySan Diego, CA
Period12/1/0612/3/06

Fingerprint

Emulation
Scale-free Networks
Complex networks
Seed
Graph in graph theory
Degree Distribution
Duplication
Network Model
Asymptotic distribution
Model

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Hormozdiari, F., Berenbrink, P., Pržulj, N., & Sahinalp, C. (2007). Not all scale free networks are born equal: The role of the seed graph in PPI network emulation. In Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers (pp. 1-13). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4532 LNBI).

Not all scale free networks are born equal : The role of the seed graph in PPI network emulation. / Hormozdiari, Fereydoun; Berenbrink, Petra; Pržulj, Nataša; Sahinalp, Cenk.

Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers. 2007. p. 1-13 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4532 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hormozdiari, F, Berenbrink, P, Pržulj, N & Sahinalp, C 2007, Not all scale free networks are born equal: The role of the seed graph in PPI network emulation. in Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4532 LNBI, pp. 1-13, Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, San Diego, CA, United States, 12/1/06.
Hormozdiari F, Berenbrink P, Pržulj N, Sahinalp C. Not all scale free networks are born equal: The role of the seed graph in PPI network emulation. In Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers. 2007. p. 1-13. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Hormozdiari, Fereydoun ; Berenbrink, Petra ; Pržulj, Nataša ; Sahinalp, Cenk. / Not all scale free networks are born equal : The role of the seed graph in PPI network emulation. Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers. 2007. pp. 1-13 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
@inproceedings{b68f80f777944ac09912e1a185ef56ef,
title = "Not all scale free networks are born equal: The role of the seed graph in PPI network emulation",
abstract = "The (asymptotic) degree distributions of the best known {"}scale free{"} network models are all similar and are independent of the seed graph used. Hence it has been tempting to assume that networks generated by these models are similar in general. In this paper we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the {"}right{"} seed graph, the duplication model captures many topological features of publicly available PPI networks very well.",
author = "Fereydoun Hormozdiari and Petra Berenbrink and Nataša Pržulj and Cenk Sahinalp",
year = "2007",
month = "12",
day = "1",
language = "English (US)",
isbn = "9783540730590",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
pages = "1--13",
booktitle = "Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers",

}

TY - GEN

T1 - Not all scale free networks are born equal

T2 - The role of the seed graph in PPI network emulation

AU - Hormozdiari, Fereydoun

AU - Berenbrink, Petra

AU - Pržulj, Nataša

AU - Sahinalp, Cenk

PY - 2007/12/1

Y1 - 2007/12/1

N2 - The (asymptotic) degree distributions of the best known "scale free" network models are all similar and are independent of the seed graph used. Hence it has been tempting to assume that networks generated by these models are similar in general. In this paper we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the "right" seed graph, the duplication model captures many topological features of publicly available PPI networks very well.

AB - The (asymptotic) degree distributions of the best known "scale free" network models are all similar and are independent of the seed graph used. Hence it has been tempting to assume that networks generated by these models are similar in general. In this paper we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the "right" seed graph, the duplication model captures many topological features of publicly available PPI networks very well.

UR - http://www.scopus.com/inward/record.url?scp=38049135038&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=38049135038&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:38049135038

SN - 9783540730590

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 1

EP - 13

BT - Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers

ER -