Literature DB >> 25014224

Degree-adjusted algorithm for prioritisation of candidate disease genes from gene expression and protein interactome.

Yichuan Wang1, Haiyang Fang1, Tinghong Yang1, Duzhi Wu1, Jing Zhao2.   

Abstract

Computational methods play an important role in the disease genes prioritisation by integrating many kinds of data sources such as gene expression, functional annotations and protein-protein interactions. However, the existing methods usually perform well in predicting highly linked genes, whereas they work quite poorly for loosely linked genes. Motivated by this observation, a degree-adjusted strategy is applied to improve the algorithm that was proposed earlier for the prediction of disease genes from gene expression and protein interactions. The authors also showed that the modified method is good at identifying loosely linked disease genes and the overall performance gets enhanced accordingly. This study suggests the importance of statistically adjusting the degree distribution bias in the background network for network-based modelling of complex diseases.

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Mesh:

Year:  2014        PMID: 25014224      PMCID: PMC8687299          DOI: 10.1049/iet-syb.2013.0038

Source DB:  PubMed          Journal:  IET Syst Biol        ISSN: 1751-8849            Impact factor:   1.615


  26 in total

1.  A human protein-protein interaction network: a resource for annotating the proteome.

Authors:  Ulrich Stelzl; Uwe Worm; Maciej Lalowski; Christian Haenig; Felix H Brembeck; Heike Goehler; Martin Stroedicke; Martina Zenkner; Anke Schoenherr; Susanne Koeppen; Jan Timm; Sascha Mintzlaff; Claudia Abraham; Nicole Bock; Silvia Kietzmann; Astrid Goedde; Engin Toksöz; Anja Droege; Sylvia Krobitsch; Bernhard Korn; Walter Birchmeier; Hans Lehrach; Erich E Wanker
Journal:  Cell       Date:  2005-09-23       Impact factor: 41.582

2.  Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

Authors:  Elena Nabieva; Kam Jim; Amit Agarwal; Bernard Chazelle; Mona Singh
Journal:  Bioinformatics       Date:  2005-06       Impact factor: 6.937

3.  Prioritizing candidate disease genes by network-based boosting of genome-wide association data.

Authors:  Insuk Lee; U Martin Blom; Peggy I Wang; Jung Eun Shim; Edward M Marcotte
Journal:  Genome Res       Date:  2011-05-02       Impact factor: 9.043

Review 4.  Human protein-protein interaction networks and the value for drug discovery.

Authors:  Heinz Ruffner; Andreas Bauer; Tewis Bouwmeester
Journal:  Drug Discov Today       Date:  2007-08-28       Impact factor: 7.851

Review 5.  Genetic mapping in human disease.

Authors:  David Altshuler; Mark J Daly; Eric S Lander
Journal:  Science       Date:  2008-11-07       Impact factor: 47.728

6.  Candidate gene prioritization by network analysis of differential expression using machine learning approaches.

Authors:  Daniela Nitsch; Joana P Gonçalves; Fabian Ojeda; Bart de Moor; Yves Moreau
Journal:  BMC Bioinformatics       Date:  2010-09-14       Impact factor: 3.169

7.  Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease.

Authors:  Michael Krauthammer; Charles A Kaufmann; T Conrad Gilliam; Andrey Rzhetsky
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-07       Impact factor: 11.205

8.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.

Authors:  Damian Szklarczyk; Andrea Franceschini; Michael Kuhn; Milan Simonovic; Alexander Roth; Pablo Minguez; Tobias Doerks; Manuel Stark; Jean Muller; Peer Bork; Lars J Jensen; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2010-11-02       Impact factor: 16.971

9.  Integrative disease classification based on cross-platform microarray data.

Authors:  Chun-Chi Liu; Jianjun Hu; Mrinal Kalakrishnan; Haiyan Huang; Xianghong Jasmine Zhou
Journal:  BMC Bioinformatics       Date:  2009-01-30       Impact factor: 3.169

10.  Network analysis of differential expression for the identification of disease-causing genes.

Authors:  Daniela Nitsch; Léon-Charles Tranchevent; Bernard Thienpont; Lieven Thorrez; Hilde Van Esch; Koenraad Devriendt; Yves Moreau
Journal:  PLoS One       Date:  2009-05-13       Impact factor: 3.240

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