Literature DB >> 12484863

Extreme self-organization in networks constructed from gene expression data.

Himanshu Agrawal1.   

Abstract

We study networks constructed from gene expression data obtained from many types of cancers. The networks are constructed by connecting vertices that belong to each others' list of K nearest neighbors, with K being an a priori selected non-negative integer. We introduce an order parameter for characterizing the homogeneity of the networks. On minimizing the order parameter with respect to K, degree distribution of the networks shows power-law behavior in the tails with an exponent of unity. Analysis of the eigenvalue spectrum of the networks confirms the presence of the power-law and small-world behavior. We discuss the significance of these findings in the context of evolutionary biological processes.

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Year:  2002        PMID: 12484863     DOI: 10.1103/PhysRevLett.89.268702

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  14 in total

1.  Statistical inference and reverse engineering of gene regulatory networks from observational expression data.

Authors:  Frank Emmert-Streib; Galina V Glazko; Gökmen Altay; Ricardo de Matos Simoes
Journal:  Front Genet       Date:  2012-02-03       Impact factor: 4.599

2.  Functional modules by relating protein interaction networks and gene expression.

Authors:  Sabine Tornow; H W Mewes
Journal:  Nucleic Acids Res       Date:  2003-11-01       Impact factor: 16.971

3.  Benchmarking regulatory network reconstruction with GRENDEL.

Authors:  Brian C Haynes; Michael R Brent
Journal:  Bioinformatics       Date:  2009-02-02       Impact factor: 6.937

4.  The role of indirect connections in gene networks in predicting function.

Authors:  Jesse Gillis; Paul Pavlidis
Journal:  Bioinformatics       Date:  2011-05-06       Impact factor: 6.937

Review 5.  Embryonic stem cell interactomics: the beginning of a long road to biological function.

Authors:  Maram Yousefi; Vahid Hajihoseini; Woojin Jung; Batol Hosseinpour; Hassan Rassouli; Bonghee Lee; Hossein Baharvand; KiYoung Lee; Ghasem Hosseini Salekdeh
Journal:  Stem Cell Rev Rep       Date:  2012-12       Impact factor: 5.739

6.  KIAA0101 interacts with BRCA1 and regulates centrosome number.

Authors:  Zeina Kais; Sanford H Barsky; Haritha Mathsyaraja; Alicia Zha; Derek J R Ransburgh; Gang He; Robert T Pilarski; Charles L Shapiro; Kun Huang; Jeffrey D Parvin
Journal:  Mol Cancer Res       Date:  2011-06-14       Impact factor: 5.852

7.  The impact of multifunctional genes on "guilt by association" analysis.

Authors:  Jesse Gillis; Paul Pavlidis
Journal:  PLoS One       Date:  2011-02-18       Impact factor: 3.240

8.  Functional connectivity in islets of Langerhans from mouse pancreas tissue slices.

Authors:  Andraž Stožer; Marko Gosak; Jurij Dolenšek; Matjaž Perc; Marko Marhl; Marjan Slak Rupnik; Dean Korošak
Journal:  PLoS Comput Biol       Date:  2013-02-28       Impact factor: 4.475

9.  Microarray missing data imputation based on a set theoretic framework and biological knowledge.

Authors:  Xiangchao Gan; Alan Wee-Chung Liew; Hong Yan
Journal:  Nucleic Acids Res       Date:  2006-03-20       Impact factor: 16.971

10.  Rank-based edge reconstruction for scale-free genetic regulatory networks.

Authors:  Guanrao Chen; Peter Larsen; Eyad Almasri; Yang Dai
Journal:  BMC Bioinformatics       Date:  2008-01-31       Impact factor: 3.169

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