Network Properties for Ranking Predicted miRNA Targets in Breast Cancer

MicroRNAs control the expression of their target genes by translational repression and transcriptional cleavage. They are involved in various biological processes including development and progression of cancer. To uncover the biological role of miRNAs it is important to identify their target genes. The small number of experimentally validated target genes makes computer prediction methods very important. However, state-of-the-art prediction tools result in a great number of putative targets with an unpredictable number of false positives. In this paper, we propose and evaluate two approaches for ranking the biological relevance of putative targets of miRNAs which are associated with breast cancer.

[1]  A. Hatzigeorgiou,et al.  A guide through present computational approaches for the identification of mammalian microRNA targets , 2006, Nature Methods.

[2]  Wen-Hsiung Li,et al.  MicroRNA regulation of human protein protein interaction network. , 2007, RNA.

[3]  Paul A. Bates,et al.  Global topological features of cancer proteins in the human interactome , 2006, Bioinform..

[4]  Byoung-Tak Zhang,et al.  miTarget: microRNA target gene prediction using a support vector machine , 2006, BMC Bioinformatics.

[5]  E. Wang,et al.  Genetic studies of diseases , 2007, Cellular and Molecular Life Sciences.

[6]  David L. Steffen,et al.  The Breast Cancer Gene Database: a collaborative information resource , 1999, Oncogene.

[7]  Xiequn Xu,et al.  Same computational analysis, different miRNA target predictions , 2007, Nature Methods.

[8]  Yi Zhao,et al.  Clustered microRNAs' coordination in regulating protein-protein interaction network , 2009, BMC Systems Biology.

[9]  C. Burge,et al.  Prediction of Mammalian MicroRNA Targets , 2003, Cell.

[10]  L. Freeman Centrality in social networks conceptual clarification , 1978 .

[11]  Frank J. Slack,et al.  The Role of MicroRNAs in Cancer , 2006, The Yale journal of biology and medicine.

[12]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[13]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[14]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .

[15]  E. Miska,et al.  MicroRNA—implications for cancer , 2007, Virchows Archiv.

[16]  C. Croce,et al.  MicroRNA gene expression deregulation in human breast cancer. , 2005, Cancer research.

[17]  H. B. Mann,et al.  On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other , 1947 .

[18]  A. Hatzigeorgiou,et al.  TarBase: A comprehensive database of experimentally supported animal microRNA targets. , 2005, RNA.

[19]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[20]  D. Lancet,et al.  GeneCards: integrating information about genes, proteins and diseases. , 1997, Trends in genetics : TIG.

[21]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.