Discovering disease-disease associations by fusing systems-level molecular data

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Žitnik, Marinka ^a   Janjić, Vuk ^b   Larminie, Chris ^c   Zupan, Blaž ^a,d   Pržulj, Nataša ^b  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c GLAXOSMITHKLINE   (United Kingdom)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASES; GENE ONTOLOGY; GENETICS; GENOMICS; HUMAN; PROCEDURES; SYSTEM ANALYSIS;

DISEASE; GENE ONTOLOGY; GENETICS; GENOMICS; HUMANS; SYSTEMS INTEGRATION;

EID: 84889679014     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep03202     Document Type: Article

References (55)

1. Schriml, L. et al. Disease Ontology: A backbone for disease semantic integration. Nucleic Acids Res. 40, D940-D946 (2012)
2. Nelson, S., Schopen, M., Savage, A., Schulman, J. & Arluk, N. The MeSH translation maintenance system: structure, interface design, and implementation. Medinfo 11, 67-69 (2004)
3. Aymé, S., Rath, A. & Bellet, B.WHOinternational classification of diseases (ICD) revision process: Incorporating rare diseases into the classification scheme: state of art. Orphanet J. Rare Dis. 5, P1 (2010)
4. Cornet, R.&DeKeizer,N. Forty years of SNOMED: A literature review.BMCMed. Inform. Decis. Mak. 8, S2 (2008)
5. Sioutos, N. et al. NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. J. Biomed. Inform. 40, 30-43 (2007) (Pubitemid 44821015)
6. Amberger, J., Bocchini, C.&Hamosh, A.Anew face and new challenges for online mendelian inheritance in man (OMIM). Hum. Mutat. 32, 564-567 (2011)
7. Loscalzo, J., Kohane, I. & Barabási, A.-L. Human disease classification in the postgenomic era: A complex systems approach to human pathobiology. Mol. Syst. Biol. 3, 124 (2007)
8. Gulbahce, N. et al. Viral perturbations of host networks reflect disease etiology. PLoS Comput. Biol. 8, e1002531 (2012)
9. Lee, D.-S. et al. The implications of human metabolic network topology for disease comorbidity. Proc. Natl. Acad. Sci. USA 105, 9880-5 (2008)
10. Goh, K.-i. et al. The human disease network. Proc. Natl. Acad. Sci. USA 104, 8685-8690 (2007) (Pubitemid 47175372)
11. Linghu, B., Snitkin, E. S., Hu, Z., Xia, Y.&Delisi, C. Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol. 10, R91 (2009)
12. Janjić, V. & Przulj, N. Biological function through network topology: A survey of the human diseasome. Brief Funct. Genomics (2012)
13. Emmert-Streib, F., Tripathi, S., Simoes, R., Hawwa, A. & Dehmer, M. The human disease network: Opportunities for classification, diagnosis and prediction of disorders and disease genes. Syst. Biomed. 1, 15-22 (2013)
14. Piro, R. M. & Di Cunto, F. Computational approaches to disease-gene prediction: Rationale, classification and successes. FEBS J. 279, 678-96 (2012)
15. Yu, S. et al. L2-norm multiple kernel learning and its application to biomedical data fusion. BMC Bioinformatics 11, 309 (2010)
16. Mostafavi, S. &Morris, Q. Combining many interaction networks to predict gene function and analyze gene lists. Proteomics 12, 1687-96 (2012)
17. Pandey, G. et al. An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS Comput. Biol. 6 (2010)
18. Lanckriet, G. R. G., De Bie, T., Cristianini, N., Jordan, M. I. & Noble, W. S. A statistical framework for genomic data fusion. Bioinformatics 20, 2626-2635 (2004) (Pubitemid 39530149)
19. Gevaert, O., De Smet, F., Timmerman, D., Moreau, Y. & De Moor, B. Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks. Bioinformatics 22, e184-90 (2006) (Pubitemid 44288285)
20. van Vliet,M.H., Horlings, H. M., van de Vijver, M. J., Reinders, M. J. T.&Wessels, L. F. A. Integration of clinical and gene expression data has a synergetic effect on predicting breast cancer outcome. PLoS One 7, e40358 (2012)
21. De Bie, T., Tranchevent, L.-C., van Oeffelen, L.M.M. & Moreau, Y. Kernel-based data fusion for gene prioritization. Bioinformatics 23, i125-32 (2007) (Pubitemid 47244393)
22. Aerts, S. et al. Gene prioritization through genomic data fusion. Nat. Biotechnol. 24, 537-544 (2006)
23. Chen Z.,Zhang W.,Integrative analysis using module-guided random forests reveals correlated genetic factors related to mouse weight
24. Chen, Z. & Zhang, W. Integrative analysis using module-guided random forests reveals correlated genetic factors related to mouse weight. PLoS Comput. Biol. 9, e1002956 (2013). 24.Z itnik, M. & Zupan, B. Data fusion by matrix factorization. (submitted) Preprint available at Arxiv:1307.0803. (2013)
25. Hidalgo, C. A., Blumm, N., Barabási, A.-L.&Christakis, N. A. Adynamic network approach for the study of human phenotypes. PLoS Comput. Biol. 5, e1000353 (2009)
26. Holst, F. G. E. et al. Low levels of fibrin-stabilizing factor (factor XIII) in human Plasmodium falciparum malaria: Correlation with clinical severity. Am. J. Trop. Med. Hyg. 60, 99-104 (1999) (Pubitemid 29066012)
27. Ashworth, A., Lord, C. J. & Reis-Filho, J. S. Genetic interactions in cancer progression and treatment. Cell 145, 30-8 (2011)
28. Ashburner, M. et al.Gene Ontology: Tool for the unification of biology. Nat. Genet. 25, 25-29 (2000) (Pubitemid 30257031)
29. Seal, R. L., Gordon, S. M., Lush, M. J., Wright, M. W. & Bruford, E. A. genenames.org: The HGNC resources in 2011. Nucleic Acids Res. 39, 514-519 (2011)
30. Brunet, J.-P., Tamayo, P., Golub, T. R. & Mesirov, J. P. Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. USA 101, 4164-4169 (2004) (Pubitemid 38405900)
31. Kim, P. M.&Tidor, B. Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Res. 13, 1706-1718 (2003) (Pubitemid 36874488)
32. Keuter, E. J. [Vitamin B complex deficiency causing the psychiatric symptoms of atypical endogenous depression]. Ned. Tijdschr. Geneeskd. 102, 1501-1503 (1958)
33. Carney, M. et al. Red cell folate concentrations in psychiatric patients. J. Affect. Disorders 19, 207-213 (1990) (Pubitemid 20209137)
34. Buob, D. & Copin, M. C. [Mixed cryoglobulinemia-associated membranoproliferative glomerulonephritis, disclosing gastric MALT lymphoma]. Ann. Pathol. 26, 267-270 (2006)
35. Skopouli, F. N., Dafni, U., Ioannidis, J. P. & Moutsopoulos, H. M. Clinical evolution, and morbidity and mortality of primary Sjogren's syndrome. Semin. Arthritis Rheu. 29, 296-304 (2000) (Pubitemid 30235981)
36. Von Vietinghoff, S., Schneider, W., Luft, F. & Kettritz, R. Crescentic glomerulonephritis and malignancy-guilty or guilt by association Nephrol. Dial. Transpl. 21, 3324-3326 (2006) (Pubitemid 44567116)
37. Tiede, D. J., Tefferi, A., Kochhar, R., Thompson, G. B. & Hay, I. D. Paraneoplastic cholestasis and hypercoagulability associated with medullary thyroid carcinoma. Resolution with tumor debulking. Cancer 73, 702-705 (1994)
38. Kohler, L. J., Gohara, A. F., Hamilton, R. W. & Reeves, R. S. Crescentic fibrillary glomerulonephritis associated with intermittent rifampin therapy for pulmonary tuberculosis. Clin. Nephrol. 42, 263-265 (1994) (Pubitemid 24317451)
39. Wen, Y. K. & Chen, M. L. Crescentic glomerulonephritis associated with miliary tuberculosis. Clin. Nephrol. 71, 310-313 (2009)
40. Refior, M. & Mees, K. Coexistence of bilateral paraganglioma of the A. carotis, thymoma and thyroid adenoma: A chance finding Laryngorhinootologie 79, 337-340 (2000)
41. Willemsen, M. H., Rensen, J. H., van Schrojenstein-Lantman de Valk, H. M., Hamel, B. C. & Kleefstra, T. Adult phenotypes in Angelman-and Rett-like syndromes. Mol. Syndromol. 2, 217-234 (2012)
42. Dagli, A., Buiting, K. & Williams, C. A. Molecular and clinical aspects of Angelman syndrome. Mol. Syndromol. 2, 100-112 (2012)
43. Heuss, D., Engelhardt, A., Gobel, H. & Neundorfer, B. Myopathological findings in interstitial myositis in type II polyendocrine autoimmune syndrome (Schmidt's syndrome). Neurol. Res. 17, 233-237 (1995)
44. Lim, V. & Clarke, B. L. Coexisting primary hyperparathyroidism and sarcoidosis cause increased Angiotensin-converting enzyme and decreased parathyroid hormone and phosphate levels. J. Clin. Endocr. Metab. 98, 1939-1945 (2013)
45. Clayton, P. T. et al. Mutations in the sterol 27-hydroxylase gene (CYP27A) cause hepatitis of infancy as well as cerebrotendinous xanthomatosis. J. Inherit. Metab. Dis. 25, 501-513 (2002) (Pubitemid 36104385)
46. Su, T. W., Wu, L. L. & Lin, C. P. The prevalence of dementia and depression in Taiwanese institutionalized leprosy patients, and the effectiveness evaluation of reminiscence therapy-a longitudinal, single-blind, randomized control study. Int. J. Geriatr. Psychiatry 27, 187-196 (2012)
47. Karmous-Benailly, H. et al. Unbalanced inherited complex chromosome rearrangement involving chromosome 8, 10, 11 and 16 in a patient with congenital malformations and delayed development. Eur. J. Med. Genet. 49, 431-438 (2006) (Pubitemid 44508679)
48. Christopoulou, G. et al. Clinical and molecular description of the prenatal diagnosis of a fetus with a maternally inherited microduplication 22q11.2 of 2.5 Mb. Gene 527, 694-697 (2013)
49. Howell, D., Bergsagel, J., Chu, R. &Meacham, L. Suppression ofHodgkin's disease in a patient with Cushing's syndrome. J. Pediatr. Hematol. Oncol. 26, 301-303 (2004) (Pubitemid 38621370)
50. Valiyil, R. & Christopher-Stine, L. Drug-related myopathies of which the clinician should be aware. Curr. Rheumatol. Rep. 12, 213-220 (2010)
51. Stark, C. et al. The BioGRID interaction database: 2011 update. Nucleic Acids Res. 39, 698-704 (2011)
52. Prieto, C., Risueno, A., Fontanillo, C. & De Las Rivas, J. Human gene coexpression landscape: Confident network derived from tissue transcriptomic profiles. PLoS One 3, e3911 (2008)
53. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109-D114 (2012)
54. Knox, C. et al. Drugbank 3.0: A comprehensive resource for 'Omics' research on drugs. Nucleic Acids Res. 39, 1035-1041 (2011)
55. Osborne, J. D. et al. Annotating the human genome with Disease Ontology. BMC Genomics 10, S6 (2009)