DEGAS: De novo discovery of dysregulated pathways in human diseases

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Ulitsky, Igor ^a,d   Krishnamurthy, Akshay ^b,e   Karp, Richard M ^c   Shamir, Ron ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INTERNATIONAL COMPUTER SCIENCE INSTITUTE   (United States)

^d WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^e Carnegie Mellon University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN 14 3 3;

ARTICLE; BIOINFORMATICS; CELL PROLIFERATION; COMPUTER PROGRAM; DISEASE COURSE; GENE CONTROL; GENETIC ALGORITHM; GENOMICS; PARKINSON DISEASE; RNA SPLICING; ALGORITHM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENERAL ASPECTS OF DISEASE; GENETICS; HUMAN; UPREGULATION;

ALGORITHMS; DISEASE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; UP-REGULATION;

EID: 78149460182     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013367     Document Type: Article

References (82)

1. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37: D885-890.
2. Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3: 78.
3. Ulitsky I, Gat-Viks I, Shamir R (2008) MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. Genome Biol 9: R1.
4. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
5. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, et al. (2002) A geneexpression signature as a predictor of survival in breast cancer. N Engl J Med 347: 1999-2009.
6. Segal E, Friedman N, Kaminski N, Regev A, Koller D (2005) From signatures to models: understanding cancer using microarrays. Nat Genet Suppl: S38-45.
7. Gutierrez A, Sanda T, Grebliunaite R, Carracedo A, Salmena L, et al. (2009) High frequency of PTEN, PI3K, and AKT abnormalities in T-cell acute lymphoblastic leukemia. Blood 114: 647-650.
8. Network TCGAR (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
9. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455: 1069-1075.
10. Inoki K, Corradetti MN, Guan KL (2005) Dysregulation of the TSC-mTOR pathway in human disease. Nat Genet 37: 19-24.
11. Zien A, Kuffner R, Zimmer R, Lengauer T (2000) Analysis of gene expression data with pathway scores. Proc Int Conf Intell Syst Mol Biol 8: 407-417.
12. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, 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.
13. Oron AP, Jiang Z, Gentleman R (2008) Gene set enrichment analysis using linear models and diagnostics. Bioinformatics 24: 2586-2591.
14. Kim SY, Volsky DJ (2005) PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 6: 144.
15. Jiang Z, Gentleman R (2007) Extensions to gene set enrichment. Bioinformatics 23: 306-313.
16. Finocchiaro G, Mancuso F, Muller H (2005) Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control. BMC Bioinformatics 6 Suppl 4: S14.
17. Lee E, Chuang HY, Kim JW, Ideker T, Lee D (2008) Inferring pathway activity toward precise disease classification. PLoS Comput Biol 4: e1000217.
18. Setlur SR, Royce TE, Sboner A, Mosquera JM, Demichelis F, et al. (2007) Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer. Cancer Res 67: 10296-10303.
19. Rapaport F, Zinovyev A, Dutreix M, Barillot E, Vert JP (2007) Classification of microarray data using gene networks. BMC Bioinformatics 8: 35.
20. Chuang HY, Lee E, Liu YT, Lee D, Ideker T (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3: 140.
21. Hart GT, Ramani AK, Marcotte EM (2006) How complete are current yeast and human protein-interaction networks? Genome Biol 7: 120.
22. Ulitsky I, Shamir R (2009) Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics 25: 1158-1164.
23. Ulitsky I, Shamir R (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 1: 8.
24. Hanisch D, Zien A, Zimmer R, Lengauer T (2002) Co-clustering of biological networks and gene expression data. Bioinformatics 18 Suppl 1: S145-154.
25. Segal E, Wang H, Koller D (2003) Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics 19 Suppl 1: i264-271.
26. Ideker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 Suppl 1: S233-240.
27. Rajagopalan D, Agarwal P (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics 21: 788-793.
28. Cabusora L, Sutton E, Fulmer A, Forst CV (2005) Differential network expression during drug and stress response. Bioinformatics 21: 2898-2905.
29. Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, et al. (2007) Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet 3: e96.
30. Bandyopadhyay S, Kelley R, Ideker T (2006) Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput. pp 354-366.
31. Breitling R, Amtmann A, Herzyk P (2004) Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics 5: 100.
32. Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 24: i223-i231.
33. Nacu S, Critchley-Thorne R, Lee P, Holmes S (2007) Gene expression network analysis and applications to immunology. Bioinformatics 23: 850-858.
34. Berger SI, Ma'ayan A, Iyengar R (2010) Systems pharmacology of arrhythmias. Sci Signal 3: ra30.
35. Oti M, Snel B, Huynen MA, Brunner HG (2006) Predicting disease genes using protein-protein interactions. J Med Genet 43: 691-698.
36. Karni S, Soreq H, Sharan R (2009) A network-based method for predicting disease-causing genes. J Comput Biol 16: 181-189.
37. Scott MS, Perkins T, Bunnell S, Pepin F, Thomas DY, et al. (2005) Identifying regulatory subnetworks for a set of genes. Mol Cell Proteomics 4: 683-692.
38. Berger SI, Posner JM, Ma'ayan A (2007) Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics 8: 372.
39. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
40. Ulitsky I, Karp RM, Shamir R (2008) Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. Lecture Notes in Computer Science; 2008. Springer. 347 p.
41. Liang WS, Reiman EM, Valla J, Dunckley T, Beach TG, et al. (2008) Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc Natl Acad Sci U S A 105: 4441-4446.
42. Moran LB, Duke DC, Deprez M, Dexter DT, Pearce RK, et al. (2006) Whole genome expression profiling of the medial and lateral substantia nigra in Parkinson's disease. Neurogenetics 7: 1-11.
43. Lesnick TG, Papapetropoulos S, Mash DC, Ffrench-Mullen J, Shehadeh L, et al. (2007) A genomic pathway approach to a complex disease: axon guidance and Parkinson disease. PLoS Genet 3: e98.
44. Estilo CL, P Oc, Talbot S, Socci ND, Carlson DL, et al. (2009) Oral tongue cancer gene expression profiling: Identification of novel potential prognosticators by oligonucleotide microarray analysis. BMC Cancer 9: 11.
45. Ye H, Yu T, Temam S, Ziober BL, Wang J, et al. (2008) Transcriptomic dissection of tongue squamous cell carcinoma. BMC Genomics 9: 69.
46. Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, et al. (2007) Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc Natl Acad Sci U S A 104: 15858-15863.
47. Sun L, Hui AM, Su Q, Vortmeyer A, Kotliarov Y, et al. (2006) Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer Cell 9: 287-300.
48. Hodges A, Strand AD, Aragaki AK, Kuhn A, Sengstag T, et al. (2006) Regional and cellular gene expression changes in human Huntington's disease brain. Hum Mol Genet 15: 965-977.
49. Allantaz F, Chaussabel D, Stichweh D, Bennett L, Allman W, et al. (2007) Blood leukocyte microarrays to diagnose systemic onset juvenile idiopathic arthritis and follow the response to IL-1 blockade. J Exp Med 204: 2131-2144.
50. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, et al. (2004) A census of human cancer genes. Nat Rev Cancer 4: 177-183.
51. Smith CL, Goldsmith CA, Eppig JT (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6: R7.
52. Lotharius J, Brundin P (2002) Pathogenesis of Parkinson's disease: dopamine, vesicles and alpha-synuclein. Nat Rev Neurosci 3: 932-942.
53. Farrer MJ (2006) Genetics of Parkinson disease: paradigm shifts and future prospects. Nat Rev Genet 7: 306-318.
54. Tan EK, Shen H, Tan JM, Lim KL, Fook-Chong S, et al. (2005) Differential expression of splice variant and wild-type parkin in sporadic Parkinson's disease. Neurogenetics 6: 179-184.
55. Beyer K, Domingo-Sabat M, Humbert J, Carrato C, Ferrer I, et al. (2008) Differential expression of alpha-synuclein, parkin, and synphilin-1 isoforms in Lewy body disease. Neurogenetics 9: 163-172.
56. Potashkin JA, Kang UJ, Loomis PA, Jodelka FM, Ding Y, et al. (2007) MPTP administration in mice changes the ratio of splice isoforms of fosB and rgs9. Brain Res 1182: 1-10.
57. Zhong N, Kim CY, Rizzu P, Geula C, Porter DR, et al. (2006) DJ-1 transcriptionally up-regulates the human tyrosine hydroxylase by inhibiting the sumoylation of pyrimidine tract-binding protein-associated splicing factor. J Biol Chem 281: 20940-20948.
58. Maracchioni A, Totaro A, Angelini DF, Di Penta A, Bernardi G, et al. (2007) Mitochondrial damage modulates alternative splicing in neuronal cells: implications for neurodegeneration. J Neurochem 100: 142-153.
59. Greene JG, Greenamyre JT, Dingledine R (2008) Sequential and concerted gene expression changes in a chronic in vitro model of parkinsonism. Neuroscience 152: 198-207.
60. Papapetropoulos S, Ffrench-Mullen J, McCorquodale D, Qin Y, Pablo J, et al. (2006) Multiregional gene expression profiling identifies MRPS6 as a possible candidate gene for Parkinson's disease. Gene Expr 13: 205-215.
61. Scherzer CR, Eklund AC, Morse LJ, Liao Z, Locascio JJ, et al. (2007) Molecular markers of early Parkinson's disease based on gene expression in blood. Proc Natl Acad Sci U S A 104: 955-960.
62. Shehadeh LA, Yu K, Wang L, Guevara A, Singer C, et al. SRRM2, a potential blood biomarker revealing high alternative splicing in Parkinson's disease. PLoS ONE 5: e9104.
63. Blalock EM, Geddes JW, Chen KC, Porter NM, Markesbery WR, et al. (2004) Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc Natl Acad Sci U S A 101: 2173-2178.
64. Shulman JM, De Jager PL (2009) Evidence for a common pathway linking neurodegenerative diseases. Nat Genet 41: 1261-1262.
65. Jang SW, Liu X, Fu H, Rees H, Yepes M, et al. (2009) Interaction of Aktphosphorylated SRPK2 with 14-3-3 mediates cell cycle and cell death in neurons. J Biol Chem 284: 24512-24525.
66. Sutherland GT, Matigian NA, Chalk AM, Anderson MJ, Silburn PA, et al. (2009) A cross-study transcriptional analysis of Parkinson's disease. PLoS ONE 4: e4955.
67. Sato S, Chiba T, Sakata E, Kato K, Mizuno Y, et al. (2006) 14-3-3eta is a novel regulator of parkin ubiquitin ligase. Embo J 25: 211-221.
68. Ostrerova N, Petrucelli L, Farrer M, Mehta N, Choi P, et al. (1999) alpha-Synuclein shares physical and functional homology with 14-3-3 proteins. J Neurosci 19: 5782-5791.
69. Ubl A, Berg D, Holzmann C, Kruger R, Berger K, et al. (2002) 14-3-3 protein is a component of Lewy bodies in Parkinson's disease-mutation analysis and association studies of 14-3-3 eta. Brain Res Mol Brain Res 108: 33-39.
70. Ichimura T, Isobe T, Okuyama T, Takahashi N, Araki K, et al. (1988) Molecular cloning of cDNA coding for brain-specific 14-3-3 protein, a protein kinase-dependent activator of tyrosine and tryptophan hydroxylases. Proc Natl Acad Sci U S A 85: 7084-7088.
71. Zhang Y, James M, Middleton FA, Davis RL (2005) Transcriptional analysis of multiple brain regions in Parkinson's disease supports the involvement of specific protein processing, energy metabolism, and signaling pathways, and suggests novel disease mechanisms. Am J Med Genet B Neuropsychiatr Genet 137B: 5-16.
72. Mitchell JA, Aronson AR, Mork JG, Folk LC, Humphrey SM, et al. (2003) Gene indexing: characterization and analysis of NLM's GeneRIFs. AMIA Annu Symp Proc. pp 460-464.
73. McKusick VA (2007) Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 80: 588-604.
74. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
75. Cormen T, Leiserson C, Rivest R, Stein C (2009) Introduction to Algorithms, Third Edition: The MIT Press.
76. Johnson D (1973) Approximation algorithms for combinatorial problems; 1973. ACM New York, NY, USA. pp 38-49.
77. Feige U (1998) A threshold of ln n for approximating set cover. Journal of the ACM (JACM) 45: 634-652.
78. Hochbaum DS (1997) Approximation algorithms for NP-hard problems. Boston: PWS Pub. Co. pp xxii, 596 p.
79. Dobson G (1982) Worst-case analysis of greedy heuristics for integer programming with nonnegative data. Mathematics of Operations Research 7: 515-531.
80. Shuai TP, Hu XD (2006) Connected set cover problem and its applications. Algorithmic Aspects in Information and Management, Proceedings 4041: 243-254.
81. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
82. Ulitsky I, Shamir R (2008) Detecting pathways transcriptionally correlated with clinical parameters. Comput Syst Bioinformatics Conf 7: 249-258.