ModuleBlast: Identifying activated sub-networks within and across species

Nucleic Acids Research

Volumn 43, Issue 3, 2015, Pages e20-

  Zinman, Guy E ^a   Naiman, Shoshana ^b   O'Dee, Dawn M ^c   Kumar, Nishant ^a   Nau, Gerard J ^c   Cohen, Haim Y ^b   Bar Joseph, Ziv ^a  

^a Carnegie Mellon University ^*  (United States)

^b BAR ILAN UNIVERSITY   (Israel)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN;

AGING; APOPTOSIS; ARTICLE; COMPUTER PROGRAM; GENE EXPRESSION; GENE INTERACTION; GENETIC ASSOCIATION; HUMAN; IMMUNE RESPONSE; INFECTION; NONHUMAN; PRIORITY JOURNAL; SPECIES COMPARISON; SPECIES DIFFERENCE; TEMPORAL ANALYSIS; VALIDATION PROCESS; ANIMAL; GENE REGULATORY NETWORK; GENETICS; MACACA; MOUSE;

MAMMALIA;

AGING; ANIMALS; APOPTOSIS; GENE REGULATORY NETWORKS; HUMANS; MACACA; MICE; SPECIES SPECIFICITY;

EID: 84936761536     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1224     Document Type: Article

References (52)

1. Ideker,T., Ozier,O., Schwikowski,B. and Siegel,A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240.
2. Liu,M., Liberzon,A., Kong,S.W., Lai,W.R., Park,P.J., Kohane,I.S. and Kasif,S. (2007) Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet., 3, e96.
3. Rajagopalan,D. and Agarwal,P. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793.
4. Nacu,S., Critchley-Thorne,R., Lee,P. and Holmes,S. (2007) Gene expression network analysis and applications to immunology. Bioinformatics, 23, 850-858.
5. Breitling,R., Amtmann,A. and Herzyk,P. (2004) Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics, 5, 100.
6. Dittrich,M.T., Klau,G.W., Rosenwald,A., Dandekar,T. and Müller,T. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, i223-i231.
7. Qiu,Y. (2008) Uncovering differentially expressed pathways with protein interaction and gene expression data. The Second International Symposium on Optimization and Systems Biology. 74-82.
8. Le,H.-S., Oltvai,Z.N. and Bar-Joseph,Z. (2010) Cross species queries of large gene expression databases. Bioinformatics, 26, 2416-2423.
9. Zinman,G., Brower-Sinning,R., Emeche,C.H., Ernst,J., Huang,G.T.-W., Mahony,S., Myers,A.J., O'Dee,D.M., Flynn,J.L., Nau,G.J. et al. (2011) Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One, 6, e22401.
10. Tirosh,I., Weinberger,A., Carmi,M. and Barkai,N. (2006) A genetic signature of interspecies variations in gene expression. Nat. Genet., 38, 830-834.
11. Bergmann,S., Ihmels,J. and Barkai,N. (2004) Similarities and differences in genome-wide expression data of six organisms. PLoS Biol., 2, 85-93.
12. Kuo,D., Tan,K., Zinman,G., Ravasi,T., Bar-Joseph,Z. and Ideker,T. (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol., 11, R77.
13. Cabusora,L., Sutton,E., Fulmer,A. and Forst,C.V (2005) Differential network expression during drug and stress response. Bioinformatics, 21, 2898-2905.
14. Faust,K., Dupont,P., Callut,J. and van Helden,J. (2010) Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics, 26, 1211-1218.
15. Guo,Z., Wang,L., Li,Y., Gong,X., Yao,C., Ma,W., Wang,D., Li,Y., Zhu,J., Zhang,M. et al. (2007) Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics, 23, 2121-2128.
16. Nacu,S., Critchley-Thorne,R., Lee,P. and Holmes,S. (2007) Gene expression network analysis and applications to immunology. Bioinformatics, 23, 850-858.
17. Sohler,F., Hanisch,D. and Zimmer,R. (2004) New methods for joint analysis of biological networks and expression data. Bioinformatics, 20, 1517-1521.
18. Breitling,R., Amtmann,A. and Herzyk,P. (2004) Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics, 5, 100.
19. Dittrich,M.T., Klau,G.W., Rosenwald,A., Dandekar,T. and Müller,T. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, i223-i231.
20. Ulitsky,I. and Shamir,R. (2009) Identifying functional modules using expression profiles and confidence-scored protein interactions - Ulitsky and Shamir. Bioinformatics, 25, 1158-1164.
21. Wu Zhao,X. and Chen,L. (2009) Identifying responsive functional modules from protein-protein interaction network. Mol. Cells, 27, 271-277.
22. Deshpande,R., Sharma,S., Verfaillie,C.M., Hu,W.-S. and Myers,C.L. (2010) A scalable approach for discovering conserved active subnetworks across species. PLoS Comput. Biol., 6, e1001028.
23. Santic,M., Al-Khodor,S. and Abu Kwaik,Y. (2010) Cell biology and molecular ecology of Francisella tularensis. Cell. Microbiol., 12, 129-139.
24. Stark,C., Breitkreutz,B.-J., Reguly,T., Boucher,L., Breitkreutz,A. and Tyers,M. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
25. Ostlund,G., Schmitt,T., Forslund,K., Köstler,T., Messina,D.N., Roopra,S., Frings,O. and Sonnhammer,E.L.L. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res., 38, D196-D203.
26. Kawahara,T.L.A., Michishita,E., Adler,A.S., Damian,M., Berber,E., Lin,M., McCord,R.A., Ongaigui,K.C.L., Boxer,L.D., Chang,H.Y. et al. (2009) SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span. Cell, 136, 62-74.
27. Rajagopalan,D. and Agarwal,P. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793.
28. Consortium,G.O. (2008) The Gene Ontology project in 2008. Nucleic Acids Res., 36, D440-D444.
29. Kanehisa,M., Goto,S., Hattori,M., Aoki-Kinoshita,K.F., Itoh,M., Kawashima,S., Katayama,T., Araki,M. and Hirakawa,M. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res., 34, D354-D357.
30. Subramanian,A., Tamayo,P., Mootha,V.K., Mukherjee,S., Ebert,B.L., Gillette,M.A., Paulovich,A., Pomeroy,S.L., Golub,T.R., Lander,E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. U.S.A., 102, 15545-15550.
31. Matthews,L., Gopinath,G., Gillespie,M., Caudy,M., Croft,D., de Bono,B., Garapati,P., Hemish,J., Hermjakob,H., Jassal,B. et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res., 37, D619-D622.
32. Matys,V., Fricke,E., Geffers,R., Gössling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
33. Saha,A., Tan,A.C. and Kang,J. (2014) Automatic context-specific subnetwork discovery from large interaction networks. PLoS One, 9, e84227.
34. Ulitsky,I. and Shamir,R. (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol., 1, 8.
35. Cline,M.S., Smoot,M., Cerami,E., Kuchinsky,A., Landys,N., Workman,C., Christmas,R., Avila-Campilo,I., Creech,M., Gross,B. et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc., 2, 2366-2382.
36. Look,D.C., Walter,M.J., Williamson,M.R., Pang,L., You,Y., Sreshta,J.N., Johnson,J.E., Zander,D.S. and Brody,S.L. (2001) Effects of paramyxoviral infection on airway epithelial cell Foxj1 expression, ciliogenesis, and mucociliary function. Am. J. Pathol., 159, 2055-2069.
37. Telepnev,M., Golovliov,I. and Sjöstedt,A. (2005) Francisella tularensis LVS initially activates but subsequently down-regulates intracellular signaling and cytokine secretion in mouse monocytic and human peripheral blood mononuclear cells. Microb. Pathog., 38, 239-247.
38. Andersson,H., Hartmanová,B., Ba¨ck,E., Eliasson,H., Landfors,M., Na¨slund,L., Rydén,P. and Sjöstedt,A. (2006) Transcriptional profiling of the peripheral blood response during tularemia. Genes Immun., 7, 503-513.
39. Paranavitana,C., Pittman,P.R., Velauthapillai,M., Zelazowska,E. and Dasilva,L. (2008) Transcriptional profiling of Francisella tularensis infected peripheral blood mononuclear cells: a predictive tool for tularemia. FEMS Immunol. Med. Microbiol., 54, 92-103.
40. Jenner,R.G. and Young,R.A. (2005) Insights into host responses against pathogens from transcriptional profiling. Nat. Rev. Microbiol., 3, 281-294.
41. Lai,X.-H. and Sjostedt,A. (2003) Delineation of the molecular mechanisms of Francisella tularensis-induced apoptosis in murine macrophages. Infect. Immun., 71, 4642-4646.
42. Santic,M., Pavokovic,G., Jones,S., Asare,R. and Kwaik,Y.A. (2010) Regulation of apoptosis and anti-apoptosis signalling by Francisella tularensis. Microbes Infect., 12, 126-134.
43. Chen,L.-F., Mu,Y. and Greene,W.C. (2002) Acetylation of RelA at discrete sites regulates distinct nuclear functions of NF-kappaB. EMBO J., 21, 6539-6548.
44. Prives,C. and Manley,J.L. (2001) Why is p53 acetylated? Cell, 107, 815-818.
45. Butchar,J.P., Cremer,T.J., Clay,C.D., Gavrilin,M.A., Wewers,M.D., Marsh,C.B., Schlesinger,L.S. and Tridandapani,S. (2008) Microarray analysis of human monocytes infected with Francisella tularensis identifies new targets of host response subversion. PLoS One, 3, e2924.
46. Barish,G.D., Downes,M., Alaynick,W.A., Yu,R.T., Ocampo,C.B., Bookout,A.L., Mangelsdorf,D.J. and Evans,R.M. (2005) A Nuclear Receptor Atlas: macrophage activation. Mol. Endocrinol., 19, 2466-2477.
47. Kanfi,Y., Shalman,R., Peshti,V., Pilosof,S.N., Gozlan,Y.M., Pearson,K.J., Lerrer,B., Moazed,D., Marine,J.-C., de Cabo,R. et al. (2008) Regulation of SIRT6 protein levels by nutrient availability. FEBS Lett., 582, 543-548.
48. Mostoslavsky,R., Chua,K.F., Lombard,D.B., Pang,W.W., Fischer,M.R., Gellon,L., Liu,P., Mostoslavsky,G., Franco,S., Murphy,M.M. et al. (2006) Genomic instability and aging-like phenotype in the absence of mammalian SIRT6. Cell, 124, 315-329.
49. Kanfi,Y., Naiman,S., Amir,G., Peshti,V., Zinman,G., Nahum,L., Bar-Joseph,Z. and Cohen,H.Y. (2012) The sirtuin SIRT6 regulates lifespan in male mice. Nature, 483, 218-221.
50. Grimley,R., Polyakova,O., Vamathevan,J., McKenary,J., Hayes,B., Patel,C., Smith,J., Bridges,A., Fosberry,A., Bhardwaja,A. et al. (2012) Over expression of wild type or a catalytically dead mutant of Sirtuin 6 does not influence NFκB responses. PLoS One, 7, e39847.
51. McGary,K.L., Park,T.J., Woods,J.O., Cha,H.J., Wallingford,J.B. and Marcotte,E.M. (2010) Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc. Natl Acad. Sci. U.S.A., 107, 6544-6549.
52. Shahin,M. and Ananth,G. (2012) Biological Network Alignment. In: Koyutürk,M., Subramaniam,S. and Grama,A. (eds). Functional coherence of molecular networks in bioinformatics. Springer, New York, pp. 97-136.