Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome

BMC Systems Biology

Volumn 2, Issue , 2008, Pages

  Presson, Angela P ^a   Sobel, Eric M ^b   Papp, Jeanette C ^b   Suarez, Charlyn J ^b   Whistler, Toni ^c   Rajeevan, Mangalathu S ^c   Vernon, Suzanne D ^c,d   Horvath, Steve ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^d The Chronic Fatigue and Immune Dysfunction Syndromes (CFIDS) Association of America   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; CHRONIC FATIGUE SYNDROME; COMPUTER PROGRAM; FEMALE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC MARKER; GENETIC SCREENING; GENETICS; HUMAN; MALE; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMS BIOLOGY;

COMPUTATIONAL BIOLOGY; FATIGUE SYNDROME, CHRONIC; FEMALE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC MARKERS; GENETIC SCREENING; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; SYSTEMS BIOLOGY;

EID: 58549117328     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-95     Document Type: Article

References (71)

1. Zhou L Ma X Sun F The effects of protein interactions, gene essentiality and regulatory regions on expression variation BMC Syst Biol 2008, 2:54. 2474594 18582382 10.1186/1752-0509-2-54
2. Shieh GS Chen CM Yu CY Huang J Wang WF Lo YC Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling BMC Bioinformatics 2008, 9:134. 2323972 18312694 10.1186/ 1471-2105-9-134
3. Wei H Persson S Mehta T Srinivasasainagendra V Chen L Page GP Somerville C Loraine A Transcriptional coordination of the metabolic network in Arabidopsis Plant Physiol 2006, 142(2):762-74. 1586052 16920875 10.1104/ pp.106.080358
4. Stuart JM Segal E Koller D Kim SK A gene-coexpression network for global discovery of conserved genetic modules Science 2003, 302(5643):249-55. 10.1126/science.1087447 12934013
5. Emilsson V Thorleifsson G Zhang B Leonardson AS Zink F Zhu J Carlson S Helgason A Walters GB Gunnarsdottir S Mouy M Steinthorsdottir V Eiriksdottir GH Bjornsdottir G Reynisdottir I Gudbjartsson D Helgadottir A Jonasdottir A Styrkarsdottir U Gretarsdottir S Magnusson KP Stefansson H Fossdal R Kristjansson K Gislason HG Stefansson T Leifsson BG Thorsteinsdottir U Lamb JR Gulcher JR Reitman ML Kong A Schadt EE Stefansson K Genetics of gene expression and its effect on disease Nature 2008, 452(7186):423-8. 10.1038/nature06758 18344981
6. Oldham MC Horvath S Geschwind DH Conservation and evolution of gene coexpression networks in human and chimpanzee brains Proc Natl Acad Sci USA 2006, 103(47):17973-8. 1693857 17101986 10.1073/pnas.0605938103
7. Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci USA 2005, 102(43):15545-50. 1239896 16199517 10.1073/pnas.0506580102
8. Zhang B Horvath S A general framework for weighted gene co-expression network analysis Stat Appl Genet Mol Biol 2005, 4:ARticle17 http://www.bepress.com/sagmb/vol4/iss1/art17/ 16646834
9. Horvath S Zhang B Carlson M Lu KV Zhu S Felciano RM Laurance MF Zhao W Qi S Chen Z Lee Y Scheck AC Liau LM Wu H Geschwind DH Febbo PG Kornblum HI Cloughesy TF Nelson SF Mischel PS Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target Proc Natl Acad Sci USA 2006, 103(46):17402-17407. 1635024 17090670 10.1073/ pnas.0608396103
10. Ghazalpour A Doss S Zhang B Wang S Plaisier C Castellanos R Brozell A Schadt EE Drake TA Lusis AJ Horvath S Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight PLoS Genet 2006, 2(8):. 1550283 16934000
11. Fuller TF Ghazalpour A Aten JE Drake TA Lusis AJ Horvath S Weighted gene coexpression network analysis strategies applied to mouse weight Mamm Genome 2007, 18(6-7):463-72. 1998880 17668265 10.1007/s00335-007-9043-3
12. Gargalovic PS Imura M Zhang B Gharavi NM Clark MJ Pagnon J Yang WP He A Truong A Patel S Nelson SF Horvath S Berliner JA Kirchgessner TG Lusis AJ Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids Proc Natl Acad Sci USA 2006, 103(34):12741-6. 1568918 16912112 10.1073/pnas.0605457103
13. Katan MB Apolipoprotein E isoforms, serum cholesterol, and cancer Lancet 1986, 1(8479):507-8. 10.1016/S0140-6736(86)92972-7 2869248
14. Clayton D McKeigue PM Epidemiological methods for studying genes and environmental factors in complex diseases Lancet 2001, 358(9290):1356-1360. 10.1016/S0140-6736(01)06418-2 11684236
15. Smith D Ebrahim S Mendelian randomization': Can genetic epidemiology contribute to understanding environmental determinants of disease? Int J Epidemiol 2003, 32:1-22. 10.1093/ije/dyg070 12689998
16. Little J Khoury M Mendelian randomization: A new spin or real progress? Lancet 2003, 362:930-931. 10.1016/S0140-6736(03)14396-6 14511923
17. Schadt EE Lamb J Yang X Zhu J Edwards S Guhathakurta D Sieberts SK Monks S Reitman M Zhang C Lum PY Leonardson A Thieringer R Metzger JM Yang L Castle J Zhu H Kash SF Drake TA Sachs A Lusis AJ An integrative genomics approach to infer causal associations between gene expression and disease Nat Genet 2005, 37(7):710-717. 10.1038/ng1589 15965475
18. Aten JE Fuller TF Lusis AJ Horvath S Using genetic markers to orient the edges in quantitative trait networks: The NEO software BMC Syst Biol 2008, 2:34. 2387136 18412962 10.1186/1752-0509-2-34
19. Chaibub Neto E Ferrara CT Attie AD Yandell BS Inferring causal phenotype networks from segregating populations Genetics 2008, 179(2):1089-100. 2429862 18505877 10.1534/genetics.107.085167
20. Opgen-Rhein R Strimmer K From correlation to causation networks: A simple approximate learning algorithm and its application to high-dimensional plant gene expression data BMC Syst Biol 2007, 1:37. 1995222 17683609 10.1186/1752-0509-1-37
21. Li R Tsaih SW Shockley K Stylianou IM Wergedal J Paigen B Churchill GA Structural model analysis of multiple quantitative traits PLoS Genet 2006, 2(7):e114. 1513264 16848643 10.1371/journal.pgen.0020114
22. Chen Y Zhu J Lum PY Yang X Pinto S MacNeil DJ Zhang C Lamb J Edwards S Sieberts SK Leonardson A Castellini LW Wang S Champy MF Zhang B Emilsson V Doss S Ghazalpour A Horvath S Drake TA Lusis AJ Schadt EE Variations in DNA elucidate molecular networks that cause disease Nature 2008, 452(7186):429-35. 10.1038/nature06757 18344982
23. Centers for Disease Control and Prevention, Chronic Fatigue Syndrome 2006 http://www.cdc.gov/cfs
24. Fukuda K Straus SE Hickie I Sharpe MC Dobbins JG Komaroff A The chronic fatigue syndrome: A comprehensive approach to its definition and study. International Chronic Fatigue Syndrome Study Group Ann Intern Med 1994, 121(12):953-9. 7978722
25. Bains W Treating Chronic Fatigue states as a disease of the regulation of energy metabolism Med Hypotheses 2008, 71(4):481-488. 10.1016/ j.mehy.2008.02.022 18684570
26. Hench PK Evaluation and differential diagnosis of fibromyalgia. Approach to diagnosis and management Rheum Dis Clin North Am 1989, 15:19-29. 2644676
27. Lloyd AR Gandevia SC Hales JP Muscle performance, voluntary activation, twitch properties and perceived effort in normal subjects and patients with the chronic fatigue syndrome Brain 1991, 114(Pt 1A):85-98. 1998892
28. Torpy DJ Chrousos GP The three-way interactions between the hypothalamic-pituitary-adrenal and gonadal axes and the immune system Baillieres Clin Rheumatol 1996, 10(2):181-98. 10.1016/ S0950-3579(96)80014-8 8911646
29. Kaushik N Fear D Richards SC McDermott CR Nuwaysir EF Kellam P Harrison TJ Wilkinson RJ Tyrrell DA Holgate ST Kerr JR Gene expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome J Clin Pathol 2005, 58(8):826-32. 1770875 16049284 10.1136/ jcp.2005.025718
30. Holmes GP Kaplan JE Stewart JA Hunt B Pinsky PF Schonberger LB A cluster of patients with a chronic mononucleosis-like syndrome. Is Epstein-Barr virus the cause? JAMA 1987, 257(17):2297-302. 10.1001/jama.257.17.2297 3033337
31. Klimas NG Koneru AO Chronic fatigue syndrome: Inflammation, immune function, and neuroendocrine interactions Curr Rheumatol Rep 2007, 9(6):482-7. 10.1007/s11926-007-0078-y 18177602
32. Rasmussen AK Nielsen H Andersen V Barington T Bendtzen K Hansen MB Nielsen L Pedersen BK Wiik A Chronic fatigue syndrome-a controlled cross sectional study J Rheumatol 1994, 21(8):1527-31. 7983659
33. Patarca R Cytokines and chronic fatigue syndrome Ann N Y Acad Sci 2001, 933:185-200. 12000020
34. Vojdani A Ghoneum M Choppa PC Magtoto L Lapp CW Elevated apoptotic cell population in patients with chronic fatigue syndrome: The pivotal role of protein kinase RNA J Intern Med 1997, 242(6):465-478. 9437407
35. Kennedy G Spence V Underwood C Belch JJ Increased neutrophil apoptosis in chronic fatigue syndrome J Clin Pathol 2004, 57(8):891-3. 1770396 15280416 10.1136/jcp.2003.015511
36. Silverman MN Pearce BD Biron CA Miller AH Immune modulation of the hypothalamic-pituitary-adrenal (HPA) axis during viral infection Viral Immunol 2005, 18:41-78. 1224723 15802953 10.1089/vim.2005.18.41
37. Rajeevan MS Smith AK Dimulescu I Unger ER Vernon SD Heim C Reeves WC Glucocorticoid receptor polymorphisms and haplotypes associated with chronic fatigue syndrome Genes Brain Behav 2007, 6(2):167-176. 10.1111/ j.1601-183X.2006.00244.x 16740143
38. Smith AK White PD Aslakson E Vollmer-Conna U Rajeevan MS Polymorphisms in genes regulating the HPA axis associated with empirically delineated classes of unexplained chronic fatigue Pharmacogenomics 2006, 7(3):387-94. 10.2217/14622416.7.3.387 16610949
39. Goertzel BN Pennachin C de Souza Coelho L Gurbaxani B Maloney EM Jones JF Combinations of single nucleotide polymorphisms in neuroendocrine effector and receptor genes predict chronic fatigue syndrome Pharmacogenomics 2006, 7(3):475-83. 10.2217/14622416.7.3.475 16610957
40. Vernon SD Reeves WC The challenge of integrating disparate high-content data: Epidemiological, clinical and laboratory data collected during an in-hospital study of chronic fatigue syndrome Pharmacogenomics 2006, 7(3):345-54. 10.2217/14622416.7.3.345 16610945
41. Whistler T Unger ER Nisenbaum R Vernon SD Integration of gene expression, clinical, and epidemiologic data to characterize Chronic Fatigue Syndrome J Transl Med 2003, 1:10. 305360 14641939 10.1186/ 1479-5876-1-10
42. Smith AK Dimulescu I Falkenberg VR Narasimhan S Heim C Vernon SD Rajeevan MS Genetic evaluation of the serotonergic system in chronic fatigue syndrome Psychoneuroendocrinology 2008, 33(2):188-97. 10.1016/ j.psyneuen.2007.11.001 18079067
43. Ferrara CT Wang P Neto EC Stevens RD Bain JR Wenner BR Ilkayeva OR Keller MP Blasiole DA Kendziorski C Yandell BS Newgard CB Attie AD Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling PLoS Genet 2008, 4(3):e1000034. 2265422 18369453 10.1371/journal.pgen.1000034
44. R Development Core Team R: A Language and Environment for Statistical Computing 2008 http://www.R-project.org
45. Horvath S Dong J Geometric interpretation of gene coexpression network analysis PLoS Comput Biol 2008, 4(8):e1000117. 2446438 18704157 10.1371/ journal.pcbi.1000117
46. Dong J Horvath S Understanding network concepts in modules BMC Syst Biol 2007, 1:24. 10.1186/1752-0509-1-24 17547772
47. Yip AM Horvath S Gene network interconnectedness and the generalized topological overlap measure BMC Bioinformatics 2007, 8:22. 1797055 17250769 10.1186/1471-2105-8-22
48. Ravasz E Somera AL Mongru DA Oltvai ZN Barabasi AL Hierarchical organization of modularity in metabolic networks Science 2002, 297(5586):1551-5. 10.1126/science.1073374 12202830
49. Li A Horvath S Network Neighborhood Analysis With The Multi-Node Topological Overlap Measure Bioinformatics 2007, 23(2):222-231. 10.1093/ bioinformatics/btl581 17110366
50. Freeman L A Set of Measures of Centrality Based on Betweenness Sociometry 1977, 40:35-41. 10.2307/3033543
51. Reyes M Nisenbaum R Hoaglin DC Unger ER Emmons C Randall B Stewart JA Abbey S Jones JF Gantz N Minden S Reeves WC Prevalence and incidence of chronic fatigue syndrome in Wichita, Kansas Arch Intern Med 2003, 163(13):1530-6. 10.1001/archinte.163.13.1530 12860574
52. Reeves WC Wagner D Nisenbaum R Jones JF Gurbaxani B Solomon L Papanicolaou DA Unger ER Vernon SD Heim C Chronic fatigue syndrome-a clinically empirical approach to its definition and study BMC Med 2005, 3:19. 1334212 16356178 10.1186/1741-7015-3-19
53. Walther DJ Peter JU Bashammakh S Hortnagl H Voits M Fink H Bader M Synthesis of serotonin by a second tryptophan hydroxylase isoform Science 2003, 299(5603):76. 10.1126/science.1078197 12511643
54. Zhang X Gainetdinov RR Beaulieu JM Sotnikova TD Burch LH Williams RB Schwartz DA Krishnan KR Caron MG Loss-of-function mutation in tryptophan hydroxylase-2 identified in unipolar major depression Neuron 2005, 45:11-6. 10.1016/j.neuron.2004.12.014 15629698
55. Lane RJ Soteriou BA Zhang H Archard LC Enterovirus related metabolic myopathy: A postviral fatigue syndrome J Neurol Neurosurg Psychiatry 2003, 74(10):1382-1386. 1757378 14570830 10.1136/jnnp.74.10.1382
56. Janal MN Ciccone DS Natelson BH Sub-typing CFS patients on the basis of 'minor' symptoms Biol Psychol 2006, 73(2):124-131. 10.1016/ j.biopsycho.2006.01.003 16473456
57. Lloyd AR Hickie I Boughton CR Spencer O Wakefield D Prevalence of chronic fatigue syndrome in an Australian population Med J Aust 1990, 153(9):522-8. 2233474
58. Kerr JR Petty R Burke B Gough J Fear D Sinclair LI Mattey DL Richards SC Montgomery J Baldwin DA Kellam P Harrison TJ Griffin GE Main J Enlander D Nutt DJ Holgate ST Gene expression subtypes in patients with chronic fatigue syndrome/myalgic encephalomyelitis J Infect Dis 2008, 197(8):1171-84. 10.1086/533453 18462164
59. Flanagan SP 'Nude', a new hairless gene with pleiotropic effects in the mouse Genet Res 1966, 8:295-309. 5980117
60. Pantelouris EM Absence of thymus in a mouse mutant Nature 1968, 217(5126):370-371. 10.1038/217370a0 5639157
61. De Sousa MA Parrott DM Pantelouris EM The lymphoid tissues in mice with congenital aplasia of the thymus Clin Exp Immunol 1969, 4(6):637-644. 1579038 5784127
62. Adriani M Martinez-Mir A Fusco F Busiello R Frank J Telese S Matrecano E Ursini MV Christiano AM Pignata C Ancestral founder mutation of the nude (FOXN1) gene in congenital severe combined immunodeficiency associated with alopecia in southern Italy population Ann Hum Genet 2004, 68(Pt 3):265-8. 10.1046/j.1529-8817.2004.00091.x 15180707
63. Pignata C Fiore M Guzzetta V Castaldo A Sebastio G Porta F Guarino A Congenital Alopecia and nail dystrophy associated with severe functional T-cell immunodeficiency in two sibs Am J Med Genet 1996, 65(2):167-70. 10.1002/(SICI)1096-8628(19961016)65:2<167::AID-AJMG17>3.0.CO;2-O 8911612
64. Chang TS Cho CS Park S Yu S Kang SW Rhee SG Peroxiredoxin III, a mitochondrion-specific peroxidase, regulates apoptotic signaling by mitochondria J Biol Chem 2004, 279(40):41975-84. 10.1074/jbc.M407707200 15280382
65. Wonsey DR Zeller KI Dang CV The c-Myc target gene PRDX3 is required for mitochondrial homeostasis and neoplastic transformation Proc Natl Acad Sci USA 2002, 99(10):6649-54. 124457 12011429 10.1073/pnas.102523299
66. Elpeleg O Miller C Hershkovitz E Bitner-Glindzicz M Bondi-Rubinstein G Rahman S Pagnamenta A Eshhar S Saada A Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion Am J Hum Genet 2005, 76(6):1081-1086. 1196446 15877282 10.1086/430843
67. Carrozzo R Dionisi-Vici C Steuerwald U Lucioli S Deodato F Di Giandomenico S Bertini E Franke B Kluijtmans LA Meschini MC Rizzo C Piemonte F Rodenburg R Santer R Santorelli FM van Rooij A Vermunt-de Koning D Morava E Wevers RA SUCLA2 mutations are associated with mild methylmalonic aciduria, Leigh-like encephalomyopathy, dystonia and deafness Brain 2007, 130(Pt 3):862-874. 10.1093/brain/awl389 17301081
68. Storey JD Tibshirani R Statistical significance for genomewide studies Proc Natl Acad Sci USA 2003, 100(16):9440-5. 170937 12883005 10.1073/ pnas.1530509100
69. Kurup RK Kurup PA Hypothalamic digoxin, cerebral chemical dominance and myalgic encephalomyelitis Int J Neurosci 2003, 113(5):683-701. 10.1080/ 00207450390200026 12745627
70. Kaasa S Knobel H Loge JH Hjermstad MJ Hodgkin's disease: Quality of life in future trials Ann Oncol 1998, 9(Suppl 5):137-45. 10.1023/ A:1008452711224 9926254
71. Reeves WC Lloyd A Vernon SD Klimas N Jason LA Bleijenberg G Evengard B White PD Nisenbaum R Unger ER Identification of ambiguities in the 1994 chronic fatigue syndrome research case definition and recommendations for resolution BMC Health Serv Res 2003, 3:25. 317472 14702202 10.1186/ 1472-6963-3-25