Biological Random Walks: Integrating heterogeneous data in disease gene prioritization

This work proposes a unified framework to leverage biological information in network propagation-based gene prioritization algorithms. Preliminary results on breast cancer data show significant improvements over state-of-the-art baselines, such as the prioritization of genes that are not identified as potential candidates by interactome-based algorithms, but that appear to be involved in/or potentially related to breast cancer, according to a functional analysis based on recent literature.

[1]  Bernhard O. Palsson,et al.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions , 2010, BMC Bioinformatics.

[2]  E. Lander,et al.  Estrogen expands breast cancer stem-like cells through paracrine FGF/Tbx3 signaling , 2010, Proceedings of the National Academy of Sciences.

[3]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[4]  Maria Victoria Schneider,et al.  Next generation of network medicine: interdisciplinary signaling approaches. , 2017, Integrative biology : quantitative biosciences from nano to macro.

[5]  G. Sledge VEGF-Targeting Therapy for Breast Cancer , 2005, Journal of Mammary Gland Biology and Neoplasia.

[6]  Haifa Dbouk,et al.  Epidemiology and prognosis of breast cancer in young women. , 2013, Journal of thoracic disease.

[7]  J. Baselga,et al.  Trastuzumab emtansine for HER2-positive advanced breast cancer. , 2012, The New England journal of medicine.

[8]  M. Todaro,et al.  p63 role in breast cancer , 2016, Aging.

[9]  A. Barabasi,et al.  Uncovering disease-disease relationships through the incomplete interactome , 2015, Science.

[10]  Arto Mannermaa,et al.  RAD50 and NBS1 are breast cancer susceptibility genes associated with genomic instability. , 2005, Carcinogenesis.

[11]  P. Robinson,et al.  Walking the interactome for prioritization of candidate disease genes. , 2008, American journal of human genetics.

[12]  A. Kallioniemi,et al.  The impact of bone morphogenetic protein 4 (BMP4) on breast cancer metastasis in a mouse xenograft model. , 2016, Cancer letters.

[13]  Daniel E. Carlin,et al.  The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. , 2018, Journal of molecular biology.

[14]  Livia Perfetto,et al.  MINT, the molecular interaction database: 2012 update , 2011, Nucleic Acids Res..

[15]  M. Newman,et al.  On the uniform generation of random graphs with prescribed degree sequences , 2003, cond-mat/0312028.

[16]  Pablo Villoslada,et al.  Modules, networks and systems medicine for understanding disease and aiding diagnosis , 2014, Genome Medicine.

[17]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[18]  Hans-Werner Mewes,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[19]  V. Soo,et al.  Disease Gene Prioritization , 2011 .

[20]  Kara Dolinski,et al.  The BioGRID Interaction Database: 2011 update , 2010, Nucleic Acids Res..

[21]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[22]  Albert-László Barabási,et al.  A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome , 2015, PLoS Comput. Biol..

[23]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[24]  Martin H. Schaefer,et al.  HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks , 2016, Nucleic Acids Res..

[25]  Daniel J. Park,et al.  Rare mutations in XRCC2 increase the risk of breast cancer. , 2012, American journal of human genetics.

[26]  The Gene Ontology Consortium,et al.  The Gene Ontology Resource: 20 years and still GOing strong , 2018, Nucleic Acids Res..

[27]  D. Stern Tyrosine kinase signalling in breast cancer: ErbB family receptor tyrosine kinases , 2000, Breast Cancer Research.

[28]  Carl Kingsford,et al.  The power of protein interaction networks for associating genes with diseases , 2010, Bioinform..

[29]  Benjamin J. Raphael,et al.  Network propagation: a universal amplifier of genetic associations , 2017, Nature Reviews Genetics.

[30]  J. Loscalzo,et al.  The Emerging Paradigm of Network Medicine in the Study of Human Disease , 2012, Circulation research.

[31]  Alan F. Scott,et al.  McKusick's Online Mendelian Inheritance in Man (OMIM®) , 2008, Nucleic Acids Res..