EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks

BMC Genomics

Volumn 17, Issue , 2016, Pages

  Sambaturu, Narmada ^a   Mishra, Madhulika ^a   Chandra, Nagasuma ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Condition specific network; Influential nodes; Network mining; Perturbation analysis; Ripple centrality

Indexed keywords

PROTEIN DERIVATIVE; TRANSCRIPTION FACTOR SP1; PARKIN; SP1 PROTEIN, HUMAN; UBIQUITIN PROTEIN LIGASE;

ALGORITHM; ARTICLE; DATA BASE; EPITRACER ALGORITHM; GENE; GENE ACTIVITY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MAPPING; GENE OVEREXPRESSION; PARK2 GENE; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; SENSITIVITY ANALYSIS; SYSTEMS BIOLOGY; BIOLOGY; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; SOFTWARE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENE KNOCKDOWN TECHNIQUES; PROTEIN INTERACTION MAPS; SOFTWARE; SP1 TRANSCRIPTION FACTOR; UBIQUITIN-PROTEIN LIGASES;

EID: 84988354927     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2792-1     Document Type: Article

References (24)

1. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL. The human disease network. Proc Natl Acad Sci. 2007; 104(21):8685-90.
2. Padiadpu J, Vashisht R, Chandra N. Protein-protein interaction networks suggest different targets have different propensities for triggering drug resistance. Syst Synth Biol. 2010; 4(4):311-22.
3. Rowland MA, Fontana W, Deeds EJ. Crosstalk and competition in signaling networks. Biophys J. 2012; 103(11):2389-98.
4. Edgar R, Domrachev M, Lash AE. Gene expression omnibus: Ncbi gene expression and hybridization array data repository. Nucleic Acids Res. 2002; 30(1):207-10.
5. Martin F, Sewer A, Talikka M, Xiang Y, Hoeng J, Peitsch MC. Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models. BMC Bioinformatics. 2014; 15(1):238.
6. Krämer A, Green J, Pollard J, Tugendreich S. Causal analysis approaches in ingenuity pathway analysis (ipa). Bioinformatics. 2013; 30(4):523-30.
7. Wang P, Lü J, Yu X. Identification of important nodes in directed biological networks: A network motif approach. PLoS ONE. 2014; 9(8):106132.
8. Kitsak M, Gallos LK, Havlin S, Liljeros F, Muchnik L, Stanley HE, Makse HA. Identification of influential spreaders in complex networks. Nat Phys. 2010; 6(11):888-93.
9. Lin DC, Xu L, Chen Y, Yan H, Hazawa M, Doan N, Said JW, Ding LW, Liu LZ, Yang H, et al. Genomic and functional analysis of the e3 ligase park2 in glioma. Cancer Res. 2015; 75(9):1815-27.
10. Oleaga C, Welten S, Belloc A, Solé A, Rodriguez L, Mencia N, Selga E, Tapias A, Noé V, Ciudad CJ. Identification of novel sp1 targets involved in proliferation and cancer by functional genomics. Biochem Pharmacol. 2012; 84(12):1581-91.
11. Khurana E, Fu Y, Chen J, Gerstein M. Interpretation of genomic variants using a unified biological network approach. PLoS Comput Biol. 2013; 9(3):1002886.
12. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in kegg. Nucleic Acids Res. 2014; 42(D1):199-205.
13. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al. Ncbi geo: archive for functional genomics data sets-update. Nucleic Acids Res. 2013; 41(D1):991-5.
14. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003; 4(2):249-64.
15. Sabidussi G. The centrality index of a graph. Psychometrika. 1966; 31(4):581-603.
16. Bondy JA, Murty USR, Vol. 290. Graph theory with applications. London: Macmillan; 1976.
17. Wang J, Duncan D, Shi Z, Zhang B. Web-based gene set analysis toolkit (webgestalt): Update 2013. Nucleic Acids Res. 2013; 41(W1):77-83.
18. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J. Cluego: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009; 25(8):1091-3.
19. Dijkstra EW. A note on two problems in connexion with graphs. Numer Math. 1959; 1(1):269-71.
20. Safran M, Dalah I, Alexander J, Rosen N, Stein TI, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, et al. Genecards version 3: the human gene integrator. Database. 2010; 2010:020.
21. Yuan W, Chen Z, Wu S, Guo J, Ge J, Yang P, Huang J. Silencing of epha2 inhibits invasion of human gastric cancer sgc-7901 cells in vitro and in vivo. Neoplasma. 2011; 59(1):105-13.
22. Salotti J, Dias MH, Koga MM, Armelin HA. Fibroblast growth factor 2 causes g2/m cell cycle arrest in ras-driven tumor cells through a src-dependent pathway. PloS ONE. 2013; 8(8):72582.
23. Shah S, King EM, Chandrasekhar A, Newton R. Roles for the mitogen-activated protein kinase (mapk) phosphatase, dusp1, in feedback control of inflammatory gene expression and repression by dexamethasone. J Biol Chem. 2014; 289(19):13667-79.
24. Lee MY, Kim HJ, Kim MA, Jee HJ, Kim AJ, Bae YS, Park JI, Chung JH, Yun J. Nek6 is involved in g2/m phase cell cycle arrest through dna damage-induced phosphorylation. Cell Cycle. 2008; 7(17):2705-9.