D-Map: Random Walking on Gene Network Inference Maps Towards differential Avenue Discovery

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 14, Issue 2, 2017, Pages 484-490

  Athanasiadis, Emmanouil ^a   Bourdakou, Marilena ^a,b   Spyrou, George ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^b UNIVERSITY OF ATHENS   (Greece)

Author keywords

Data and knowledge visualization; graphs and networks; inference networks; random walks

Indexed keywords

DATA VISUALIZATION; GENES; INTERFACE STATES; NEURODEGENERATIVE DISEASES; RANDOM PROCESSES; WEB CRAWLER;

CELLULAR INTERACTION; DATA AND KNOWLEDGE VISUALIZATIONS; GENE NETWORK INFERENCE; GRAPHS AND NETWORKS; INFERENCE NETWORK; RANDOM WALK; RANDOM WALK SIMULATION; RECONSTRUCTION METHOD;

GENE EXPRESSION;

PROTEIN;

ALZHEIMER DISEASE; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; HUMAN; METABOLISM; NEOPLASM; PROCEDURES; SOFTWARE;

ALZHEIMER DISEASE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; MODELS, GENETIC; NEOPLASMS; PROTEINS; SOFTWARE;

EID: 85017150661     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2016.2535267     Document Type: Article

References (38)

1. K. Mitra, A. R. Carvunis, S. K. Ramesh, and T. Ideker, "Integrative approaches for finding modular structure in biological networks, " Nature Rev. Genet., vol. 14, pp. 719-732, 2013.
2. A. Vinayagam, J. Zirin, C. Roesel, Y. Hu, B. Yilmazel, et al., "Integrating protein-protein interaction networks with phenotypes reveals signs of interactions, " Nature Methods, vol. 11, pp. 94-99, 2014.
3. J. West, G. Bianconi, S. Severini, and S. Teschendorff, "Differential network entropy reveals cancer system hallmarks, " Sci. Rep. 2, 2012, Art. no. 802, Doi: 10.1038/srep00802.
4. B. Barzel and A. L. Barabasi, "Network link prediction by global silencing of indirect correlations, " Nature Biotechnol., vol. 31, pp. 720-725, 2013.
5. J. Wieczorek, Malik-R. S. Sheriff, Y. Fermin, H. E. Grecco, E. Zamir, et al., "Uncovering distinct protein-network topologies in heterogeneous cell populations, " BMC Syst. Biol., vol. 9, no. 1, Art. no. 24, 2015.
6. T. Huan, et al., "Integrative network analysis reveals molecular mechanisms of blood pressure regulation, " Molecular Syst. Biol., vol. 11, no. 4, pp. 1-15, 2015.
7. R. Arroyo, et al., "Systematic identification of molecular links between core and candidate genes in breast cancer, " J. Molecular Biol., vol. 427, no. 6, pp. 1436-1450, 2015.
8. J. J. Faith, B. Hayete, J. T. Thaden, I. Mogno, J. Wierzbowski, et al., "Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles, " PLoS Biol., vol. 5, p. e8, 2007.
9. G. Sales and C. Romualdi, "Parmigene-A parallel R package for mutual information estimation and gene network reconstruction, " Bioinf., vol. 27, pp. 1876-1877, 2011.
10. P. E. Meyer, F. Lafitte, and G. Bontempi, "Minet: A R/Bioconductor pack-age for inferring large transcriptional networks using mutual information, " BMC Bioinf., vol. 9, p. 461, 2008.
11. A. A. Margolin, I. Nemenman, K. Basso, et al., "ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context, " BMC Bioinf., vol. 7, (Suppl 1):S7, 2006, doi: 10.1186/1471-2105-7-S1-S7.
12. P. Langfelder and S. Horvath, "WGCNA: An R package for weighted correlation network analysis, " BMC Bioinf., vol. 9, p. 559, 2008.
13. A. V. Werhli, M. Grzegorczyk, and D. Husmeier, "Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks, " Bioinf., vol. 22, pp. 2523-2531, 2006.
14. K. Komurov, S. Dursun, S. Erdin, and P. T. Ram, "NetWalker: A contextual network analysis tool for functional genomics, " BMC Genomics, vol. 13, p. 282, 2012.
15. D. Petrochilos, A. Shojaie, J. Gennari, and N. Abernethy, "Using random walks to identify cancer-associated modules in expression data, " BioData Min., vol. 6, p. 17, 2013.
16. K. R. Brown, Otasek D., M. Ali, M. J. McGuffin, W. Xie, et al., "NAViGaTOR: Network analysis, visualization and graphing Toronto, " Bioinf., vol. 25, pp. 3327-3329, 2009.
17. M. E. Smoot, K. Ono, J. Ruscheinski, P. L. Wang, and T. Ideker, "Cytoscape 2.8: New features for data integration and network visualization, " Bioinf., vol. 27, pp. 431-432, 2011.
18. M. Secrier, G. A. Pavlopoulos, J. Aerts, and R. Schneider, "Arena3D: Visualizing time-driven phenotypic differences in biological systems, " BMC Bioinf., vol. 13, p. 45, 2012.
19. A. Franceschini, D. Szklarczyk, S. Frankild, M. Kuhn, M. Simonovic et al., "STRING v9.1: Protein-protein interaction networks, with increased cover-age and integration, " Nucleic Acids Res., vol. 41, pp. D808-D815, 2013.
20. T. Barrett, S. E. Wilhite, P. Ledoux, C. Evangelista, I. F. Kim, et al., "NCBI GEO: Archive for functional genomics data sets-update, " Nucleic Acids Res., vol. 41, pp. D991-D995, 2013.
21. G. Csardi and T. Nepusz, "The igraph software package for complex network research, " InterJournal, vol. Complex Systems, 2006, pp. 1695-1704.
22. G. Altay and F. Emmert-Streib, "Structural influence of gene networks on their inference: Analysis of C3NET, " Biol. Direct, vol. 6, p. 31, 2011.
23. R. Zhong, J. D. Allen, G. Xiao, and Y. Xie, "Ensemble-based network aggregation improves the accuracy of gene network reconstruction, " PLoS One, vol. 9, p. e106319, 2014.
24. S. W. Zhang, D. D. Shao, S. Y. Zhang, and Y. B. Wang, "Prioritization of candidate disease genes by enlarging the seed set and fusing information of the network topology and gene expression, " Mol. Biosyst., vol. 10, pp. 1400-1408, 2014.
25. E. I. Athanasiadis, et al., "ZoomOut: Analyzing multiple networks as single nodes, " IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 12, no. 5, pp. 1213-1216, Sep./Oct. 2015, doi: 10.1109/TCBB.2015.2424411.
26. J. Jourquin, D. Duncan, Z. Shi, and B. Zhang, "GLAD4U: Deriving and pri-oritizing gene lists from PubMed literature, " BMC Genomics, vol. 13, (Suppl8), p. S20, 2012.
27. Koschtzki D. and F. Schreiber, "Centrality analysis methods for biological networks and their application to gene regulatory networks, " Gene Reg. Syst. Biol., vol. 2, pp. 193-201, 2008.
28. R. Saito, M. E. Smoot, K. Ono, J. Ruscheinski, P. L. Wang, S. Lotia, A. R. Pico, G. D. Bader, and T. Ideker, "A travel guide to cytoscape plugins, " Nature Methods, vol. 9, pp. 1069-1076, 2012.
29. K. Zuberi, M. Franz, H. Rodriguez, J. Montojo, C. T. Lopes, G. D. Bader, and Q. Morris, "GeneMANIA prediction server 2013 update, " Nucleic Acids Res., vol. 41, pp. W115-W122, 2013.
30. M. H. Cheok, W. Yang, C. H. Pui, J. R. Downing, C. Cheng, C. W. Naeve, and M. V. Relling, "Evans WE; Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells, " Nature Genetics, vol. 34, pp. 85-90, 2003.
31. C. Hatzis, L. Pusztai, V. Valero, D. J. Booser, L. Esserman, et al., "A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer" J. Amer. Med. Assoc., vol. 305, pp. 1873-1881, 2011.
32. D. Merico, R. Isserlin, O. Stueker, A. Emili, and G. D. Bader, "Enrichment map: A network-based method for gene-set enrichment visualization and interpretation, " PLoS One, vol. 5, p. e13984, 2010.
33. V. R. Iyer, M. B. Eisen, D. T. Ross, G. Schuler, T. Moore, et al., "The tran-scriptional program in the response of human fibroblasts to serum, " Science, vol. 283, pp. 83-87, 1999.
34. S. Rousseaux, A. Debernardi, B. Jacquiau, A. L. Vitte, A. Vesin, et al., "Ectopic activation of germline and placental genes identifies aggressive metastasis-prone lung cancers, " Sci. Translational Med., vol. 5, no. 186, 2013, Art. no. 186ra66.
35. M. Filipits, M. Rudas, R. Jakesz, P. Dubsky, F. Fitzal, et al., "A new molecular predictor of distant recurrence in ER-positive, HER2-negative breast cancer adds independent information to conventional clinical risk factors, " Clin. Cancer Res., vol. 17, pp. 6012-6020, 2011.
36. E. S. Lee, D. S. Son, S. H. Kim, J. Lee, J. Jo, et al., "Prediction of recurrence-free survival in postoperative non-small cell lung cancer patients by using an integrated model of clinical information and gene expression, " Clin. Cancer Res., vol. 14, pp. 7397-7404, 2008.
37. V. Popovici, W. Chen, B. G. Gallas, C. Hatzis, W. Shi, et al., "Effect of training-sample size and classification difficulty on the accuracy of genomic predictors, " Breast Cancer Res., vol. 12, p. R5, 2010.
38. H. R. Wong, N. Cvijanovich, R. Lin, G. L. Allen, N. J. Thomas, et al., "Identification of pediatric septic shock subclasses based on genome-wide expression profiling, " BMC Med., vol. 7, 2009, Art. no. 34.