References

• 1. 1)
     • 53. Gray, K.A., Yates, B., Seal, R.L., et al: ‘Genenames.org: the HGNC resources in 2015’, Nucleic Acids Res., 2015, 43, (Database issue), pp. D1079–D1085.
  2. 2)
     • 1. Robinson, C.V., Sali, A., Baumeister, W.: ‘The molecular sociology of the cell’, Nature, 2007, 450, (7172), pp. 973–982.
  3. 3)
     • 38. Kanehisa, M., Furumichi, M., Tanabe, M., et al: ‘KEGG: new perspectives on genomes, pathways, diseases and drugs’, Nucleic Acids Res., 2017, 45, (D1), pp. D353–D361.
  4. 4)
     • 22. Park, S., Yang, J.S., Shin, Y.E., et al: ‘Protein localization as a principal feature of the etiology and comorbidity of genetic diseases’, Mol. Syst. Biol., 2011, 7, p. 494.
  5. 5)
     • 24. Veres, D.V., Gyurko, D.M., Thaler, B., et al: ‘ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis’, Nucleic Acids Res., 2015, 43, (Database issue), pp. D485–D493.
  6. 6)
     • 31. Yousefi, S., Perozzo, R., Schmid, I., et al: ‘Calpain-mediated cleavage of Atg5 switches autophagy to apoptosis’, Nat. Cell Biol., 2006, 8, (10), pp. 1124–1132.
  7. 7)
     • 47. Dong, J., Horvath, S.: ‘Understanding network concepts in modules’, BMC Syst. Biol., 2007, 1, p. 24.
  8. 8)
     • 17. Rhee, D.Y., Cho, D.Y., Zhai, B., et al: ‘Transcription factor networks in drosophila melanogaster’, Cell Rep., 2014, 8, (6), pp. 2031–2043.
  9. 9)
     • 10. Dittrich, M.T., Klau, G.W., Rosenwald, A., et al: ‘Identifying functional modules in protein-protein interaction networks: an integrated exact approach’, Bioinformatics, 2008, 24, (13), pp. i223–i231.
  10. 10)
      • 5. Jiang, W., Zhang, Y., Meng, F., et al: ‘Identification of active transcription factor and mirna regulatory pathways in Alzheimer's disease’, Bioinformatics, 2013, 29, (20), pp. 2596–2602.
  11. 11)
      • 11. Li, X., Wu, M., Kwoh, C.K., et al: ‘Computational approaches for detecting protein complexes from protein interaction networks: a survey’, BMC Genomics, 2010, 11, (Suppl 1), p. S3.
  12. 12)
      • 45. Liberzon, A., Birger, C., Thorvaldsdottir, H., et al: ‘The molecular signatures database (MSigDB) hallmark gene set collection’, Cell Syst., 2015, 1, (6), pp. 417–425.
  13. 13)
      • 40. Mi, H., Huang, X., Muruganujan, A., et al: ‘Panther version 11: expanded annotation data from gene ontology and reactome pathways, and data analysis tool enhancements’, Nucleic Acids Res., 2017, 45, (D1), pp. D183–D189.
  14. 14)
      • 6. Hao, D., Li, C., Zhang, S., et al: ‘Network-based analysis of genotype-phenotype correlations between different inheritance modes’, Bioinformatics, 2014, 30, (22), pp. 3223–3231.
  15. 15)
      • 13. Wang, Y., Qian, X.: ‘Functional module identification in protein interaction networks by interaction patterns’, Bioinformatics, 2014, 30, (1), pp. 81–93.
  16. 16)
      • 12. Shih, Y.K., Parthasarathy, S.: ‘Identifying functional modules in interaction networks through overlapping Markov clustering’, Bioinformatics, 2012, 28, (18), pp. i473–i479.
  17. 17)
      • 51. Sims, R.J.3rd, Mandal, S.S., Reinberg, D.: ‘Recent highlights of RNA-polymerase-II-mediated transcription’, Curr. Opin. Cell Biol., 2004, 16, (3), pp. 263–271.
  18. 18)
      • 4. Koh, G.C., Porras, P., Aranda, B., et al: ‘Analyzing protein-protein interaction networks’, J. Proteome Res., 2012, 11, (4), pp. 2014–2031.
  19. 19)
      • 23. Barabasi, A.L., Oltvai, Z.N.: ‘Network biology: understanding the cell's functional organization’, Nat. Rev. Genet., 2004, 5, (2), pp. 101–113.
  20. 20)
      • 32. Wang, Y., Qian, X.: ‘Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction’, BMC Syst. Biol., 2017, 11, (Suppl 3), p. 22.
  21. 21)
      • 50. Huang, L., Guan, R.J., Pardee, A.B.: ‘Evolution of transcriptional control from prokaryotic beginnings to eukaryotic complexities’, Crit. Rev. Eukaryot Gene. Expr., 1999, 9, (3–4), pp. 175–182.
  22. 22)
      • 15. Li, T., Wernersson, R., Hansen, R.B., et al: ‘A scored human protein-protein interaction network to catalyze genomic interpretation’, Nat. Methods, 2017, 14, (1), pp. 61–64.
  23. 23)
      • 48. Marquez, R.T., Xu, L.: ‘Bcl-2:Beclin 1 complex: multiple, mechanisms regulating autophagy/apoptosis toggle switch’, Am. J. Cancer Res., 2012, 2, (2), pp. 214–221.
  24. 24)
      • 29. Tasdemir, E., Chiara Maiuri, M., Morselli, E., et al: ‘A dual role of P53 in the control of autophagy’, Autophagy, 2008, 4, (6), pp. 810–814.
  25. 25)
      • 27. Maiuri, M.C., Zalckvar, E., Kimchi, A., et al: ‘Self-eating and self-killing: crosstalk between autophagy and apoptosis’, Nat. Rev. Mol. Cell Biol., 2007, 8, (9), pp. 741–752.
  26. 26)
      • 20. Hao, N., O'Shea, E.K.: ‘Signal-dependent dynamics of transcription factor translocation controls gene expression’, Nat. Struct. Mol. Biol., 2011, 19, (1), pp. 31–39.
  27. 27)
      • 30. Tasdemir, E., Maiuri, M.C., Galluzzi, L., et al: ‘Regulation of autophagy by cytoplasmic P53’, Nat. Cell Biol., 2008, 10, (6), pp. 676–687.
  28. 28)
      • 44. Liberzon, A.: ‘A description of the molecular signatures database (MSigDB) web site’, Methods Mol. Biol., 2014, 1150, pp. 153–160.
  29. 29)
      • 7. Qin, J., Li, M.J., Wang, P., et al: ‘Proteomirexpress: inferring microrna and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data’, Mol. Cell Proteomics, 2013, 12, (11), pp. 3379–3387.
  30. 30)
      • 36. Ruepp, A., Waegele, B., Lechner, M., et al: ‘CORUM: the comprehensive resource of mammalian protein complexes--2009’, Nucleic Acids Res., 2010, 38, (Database issue), pp. D497–D501.
  31. 31)
      • 39. Kanehisa, M., Goto, S.: ‘KEGG: kyoto encyclopedia of genes and genomes’, Nucleic Acids Res., 2000, 28, (1), pp. 27–30.
  32. 32)
      • 56. Yi, Y., Zhao, Y., Li, C., et al: ‘Raid V2.0: an updated resource of RNA-associated interactions across organisms’, Nucleic Acids Res., 2017, 45, (D1), pp. D115–D118.
  33. 33)
      • 18. Zhang, T., Tan, P., Wang, L., et al: ‘Rnalocate: a resource for RNA subcellular localizations’, Nucleic Acids Res., 2016, 45, (D1), pp. D135–D138.
  34. 34)
      • 8. Lievens, S., Van der Heyden, J., Masschaele, D., et al: ‘Proteome-scale binary interactomics in human cells’, Mol. Cell Proteomics, 2016, 15, (12), pp. 3624–3639.
  35. 35)
      • 41. Thomas, P.D., Campbell, M.J., Kejariwal, A., et al: ‘Panther: a library of protein families and subfamilies indexed by function’, Genome Res., 2003, 13, (9), pp. 2129–2141.
  36. 36)
      • 9. Cheng, L., Fan, K., Huang, Y., et al: ‘Full characterization of localization diversity in the human protein interactome’, J. Proteome Res., 2017, 16, (8), pp. 3019–3029.
  37. 37)
      • 52. Baillat, D., Hakimi, M.A., Naar, A.M., et al: ‘Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II’, Cell, 2005, 123, (2), pp. 265–276.
  38. 38)
      • 57. Hu, X., Wu, Y., Lu, Z.J., et al: ‘Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations’, Brief Bioinf., 2016, 17, (6), pp. 1032–1043.
  39. 39)
      • 28. Marino, G., Niso-Santano, M., Baehrecke, E.H., et al: ‘Self-consumption: the interplay of autophagy and apoptosis’, Nat. Rev. Mol. Cell Biol., 2014, 15, (2), pp. 81–94.
  40. 40)
      • 35. Ruepp, A., Brauner, B., Dunger-Kaltenbach, I., et al: ‘CORUM: the comprehensive resource of mammalian protein complexes’, Nucleic Acids Res., 2008, 36, (Database issue), pp. D646–D650.
  41. 41)
      • 54. Cheng, L., Lo, L.Y., Tang, N.L., et al: ‘CrossNorm: a novel normalization strategy for microarray data in cancers’, Sci. Rep., 2016, 6, pp. 18898.
  42. 42)
      • 49. Pattingre, S., Tassa, A., Qu, X., et al: ‘Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy’, Cell, 2005, 122, (6), pp. 927–939.
  43. 43)
      • 33. Enright, A.J., Van Dongen, S., Ouzounis, C.A.: ‘An efficient algorithm for large-scale detection of protein families’, Nucleic Acids Res., 2002, 30, (7), pp. 1575–1584.
  44. 44)
      • 19. An, S., Kumar, R., Sheets, E.D., et al: ‘Reversible compartmentalization of de novo purine biosynthetic complexes in living cells’, Science, 2008, 320, (5872), pp. 103–106.
  45. 45)
      • 34. Papin, J.A., Hunter, T., Palsson, B.O., et al: ‘Reconstruction of cellular signalling networks and analysis of their properties’, Nat. Rev. Mol. Cell Biol., 2005, 6, (2), pp. 99–111.
  46. 46)
      • 26. Li, Y., Zhuang, L., Wang, Y., et al: ‘Connect the dots: a systems level approach for analyzing the mirna-mediated cell death network’, Autophagy, 2013, 9, (3), pp. 436–439.
  47. 47)
      • 2. Yu, H., Braun, P., Yildirim, M.A., et al: ‘High-quality binary protein interaction map of the yeast interactome network’, Science, 2008, 322, (5898), pp. 104–110.
  48. 48)
      • 3. Vidal, M., Cusick, M.E., Barabasi, A.L.: ‘Interactome networks and human disease’, Cell, 2011, 144, (6), pp. 986–998.
  49. 49)
      • 21. Casey, J.R., Grinstein, S., Orlowski, J.: ‘Sensors and regulators of intracellular pH’, Nat. Rev. Mol. Cell Biol., 2010, 11, (1), pp. 50–61.
  50. 50)
      • 14. Pizzuti, C., Rombo, S.E.: ‘Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods’, Bioinformatics, 2014, 30, (10), pp. 1343–1352.
  51. 51)
      • 42. Croft, D., O'Kelly, G., Wu, G., et al: ‘Reactome: a database of reactions, pathways and biological processes’, Nucleic Acids Res., 2011, 39, (Database issue), pp. D691–D697.
  52. 52)
      • 55. Cheng, L., Wang, X., Wong, P.K., et al: ‘ICN: a normalization method for gene expression data considering the over-expression of informative genes’, Mol. Biosyst., 2016, 12, (10), pp. 3057–3066.
  53. 53)
      • 37. Kikugawa, S., Nishikata, K., Murakami, K., et al: ‘PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-invitational protein-protein interactions integrative dataset’, BMC Syst. Biol., 2012, 6, (Suppl 2), p. S7.
  54. 54)
      • 25. Fuchs, Y., Steller, H.: ‘Programmed cell death in animal development and disease’, Cell, 2011, 147, (4), pp. 742–758.
  55. 55)
      • 43. Joshi-Tope, G., Gillespie, M., Vastrik, I., et al: ‘Reactome: a knowledgebase of biological pathways’, Nucleic Acids Res., 2005, 33, (Database issue), pp. D428–D432.
  56. 56)
      • 16. Nepusz, T., Yu, H., Paccanaro, A.: ‘Detecting overlapping protein complexes in protein-protein interaction networks’, Nat. Methods, 2012, 9, (5), pp. 471–472.
  57. 57)
      • 46. Shannon, P., Markiel, A., Ozier, O., et al: ‘Cytoscape: a software environment for integrated models of biomolecular interaction networks’, Genome Res., 2003, 13, (11), pp. 2498–2504.