Partial correlation network analyses to detect altered gene interactions in human disease: Using preeclampsia as a model

Human Genetics

Volumn 129, Issue 1, 2011, Pages 25-34

  Johansson, Åsa ^a,b   Løset, Mari ^a   Mundal, Siv B ^a   Johnson, Matthew P ^b   Freed, Katy A ^b   Fenstad, Mona H ^a   Moses, Eric K ^b   Austgulen, Rigmor ^a   Blangero, John ^b  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^b SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALBUMIN; COMPLEMENT FACTOR H; EPIDERMAL GROWTH FACTOR; EPIDERMAL GROWTH FACTOR 7; FOLLICULOGENESIS SPECIFIC BASIC HELIX LOOP HELIX PROTEIN; NICOTINAMIDE ADENINE DINUCLEOTIDE SYNTHETASE 1; SYNTHETASE; TRANSCRIPTION FACTOR HES 1; UNCLASSIFIED DRUG;

ARTICLE; CLINICAL ARTICLE; CORRELATION COEFFICIENT; DISEASE MODEL; FEMALE; GENE EXPRESSION; GENE INTERACTION; GENETIC SUSCEPTIBILITY; HUMAN; INFANT; MALE; MUTATION; PREECLAMPSIA; PRIORITY JOURNAL; TISSUE; TRANSCRIPTION REGULATION;

FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; INFANT, NEWBORN; MALE; MODELS, GENETIC; PRE-ECLAMPSIA; PREGNANCY; TRANSCRIPTION, GENETIC;

EID: 78651247734     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-010-0893-5     Document Type: Article

References (45)

1. J Ahn K Yu R Stolzenberg-Solomon KC Simon ML McCullough L Gallicchio EJ Jacobs A Ascherio K Helzlsouer KB Jacobs Q Li SJ Weinstein M Purdue J Virtamo R Horst W Wheeler S Chanock DJ Hunter RB Hayes P Kraft D Albanes 2010 Genome-wide association study of circulating vitamin D levels Hum Mol Genet 19 2739 2745 10.1093/hmg/ddq155 1:CAS:528:DC%2BC3cXntlGjsrw%3D 10.1093/hmg/ddq155 20418485
2. RA Bayne SJ Martins da Silva RA Anderson 2004 Increased expression of the FIGLA transcription factor is associated with primordial follicle formation in the human fetal ovary Mol Hum Reprod 10 373 381 1:CAS:528:DC%2BD2cXjvVSisr4%3D 10.1093/molehr/gah056 15044608 (Pubitemid 38714369)
3. LM Boccia D Lillicrap K Newcombe CR Mueller 1996 Binding of the Ets factor GA-binding protein to an upstream site in the factor IX promoter is a critical event in transactivation Mol Cell Biol 16 1929 1935 1:CAS:528:DyaK28XisFeks74%3D 8628259
4. LM Bodnar JM Catov HN Simhan MF Holick RW Powers JM Roberts 2007 Maternal vitamin D deficiency increases the risk of preeclampsia J Clin Endocrinol Metab 92 3517 3522 10.1210/jc.2007-0718 1:CAS:528:DC%2BD2sXhtVGqsrnI 10.1210/jc.2007-0718 17535985 (Pubitemid 47435329)
5. L Cobellis A Mastrogiacomo E Federico MT Schettino M De Falco L Manente G Coppola M Torella N Colacurci A De Luca 2007 Distribution of Notch protein members in normal and preeclampsia-complicated placentas Cell Tissue Res 330 527 534 10.1007/s00441-007-0511-6 1:CAS:528:DC%2BD2sXht1yis7zK 10.1007/s00441-007- 0511-6 17955263 (Pubitemid 350098221)
6. ML Cooper HO Adami H Gronberg F Wiklund FR Green MP Rayman 2008 Interaction between single nucleotide polymorphisms in selenoprotein P and mitochondrial superoxide dismutase determines prostate cancer risk Cancer Res 68 10171 10177 1:CAS:528:DC%2BD1cXhsV2it7fE 10.1158/0008-5472.CAN-08-1827 19074884
7. A de la Fuente N Bing I Hoeschele P Mendes 2004 Discovery of meaningful associations in genomic data using partial correlation coefficients Bioinformatics 20 3565 3574 10.1093/bioinformatics/bth445 (Pubitemid 40136792)
8. AO Edwards R Ritter 3rd KJ Abel A Manning C Panhuysen LA Farrer 2005 Complement factor H polymorphism and age-related macular degeneration Science 308 421 424 10.1126/science.1110189 1:CAS:528:DC%2BD2MXjtFOntLw%3D 10.1126/science.1110189 15761121 (Pubitemid 40530082)
9. Enquobahrie DA, Meller M, Rice K, Psaty BM, Siscovick DS, Williams MA (2008) Differential placental gene expression in preeclampsia. Am J Obstet Gynecol 199:566 e1-e11
10. KM Eyster CJ Mark R Gayle DS Martin 2007 The effects of estrogen and testosterone on gene expression in the rat mesenteric arteries Vascul Pharmacol 47 238 247 1:CAS:528:DC%2BD2sXhtFSlurfO 10.1016/j.vph.2007.06.007 17652031 (Pubitemid 47451827)
11. Fenstad MH, Johnson MP, Loset M, Mundal SB, Roten LT, Eide IP, Bjorge L, Sande RK, Johansson AK, Dyer TD, Forsmo S, Blangero J, Moses EK, Austgulen R (2010) STOX2 but not STOX1 is differentially expressed in decidua from preeclamptic women. Mol Hum Reprod. doi: 10.1093/molehr/gaq064
12. A Fujita JR Sato HM Garay-Malpartida R Yamaguchi S Miyano MC Sogayar CE Ferreira 2007 Modeling gene expression regulatory networks with the sparse vector autoregressive model BMC Syst Biol 1 39 10.1186/1752-0509-1-39 17761000 (Pubitemid 350047572)
13. RW Gifford PA August G Cunningham LA Green MD Lindheimer D McNellis JM Roberts BM Sibai SJ Taler 2000 Report of the National High Blood Pressure Education Program Working Group on high blood pressure in pregnancy Am J Obstet Gynecol 183 S1 S22 10.1067/mob.2000.107928 (Pubitemid 30626063)
14. RL Goldenberg DJ Rouse 1998 Prevention of premature birth N Engl J Med 339 313 320 1:STN:280:DyaK1czjsF2ktw%3D%3D 10.1056/NEJM199807303390506 9682045 (Pubitemid 28366421)
15. HH Goring JE Curran MP Johnson TD Dyer J Charlesworth SA Cole JB Jowett LJ Abraham DL Rainwater AG Comuzzie MC Mahaney L Almasy JW MacCluer AH Kissebah GR Collier EK Moses J Blangero 2007 Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes Nat Genet 39 1208 1216 10.1038/ng2119 17873875 (Pubitemid 47482685)
16. WB Grant 2010 Low vitamin D may explain the link between preeclampsia and cardiovascular disease Am Heart J 159 e19 10.1016/j.ahj.2009.12.007 10.1016/j.ahj.2009.12.007 20211290
17. JL Haines MA Hauser S Schmidt WK Scott LM Olson P Gallins KL Spencer SY Kwan M Noureddine JR Gilbert N Schnetz-Boutaud A Agarwal EA Postel MA Pericak-Vance 2005 Complement factor H variant increases the risk of age-related macular degeneration Science 308 419 421 10.1126/science.1110359 1:CAS:528:DC%2BD2MXjtFOntL8%3D 10.1126/science.1110359 15761120 (Pubitemid 40530081)
18. L Han J Zhu 2008 Using matrix of thresholding partial correlation coefficients to infer regulatory network Biosystems 91 158 165 1:CAS:528:DC%2BD1cXhtFShug%3D%3D 10.1016/j.biosystems.2007.08.008 17919808 (Pubitemid 350297571)
19. Y Hochberg Y Benjamini 1990 More powerful procedures for multiple significance testing Stat Med 9 811 818 1:STN:280:DyaK3M%2FhvFSgsA%3D%3D 10.1002/sim.4780090710 2218183
20. J Huntriss R Gosden M Hinkins B Oliver D Miller AJ Rutherford HM Picton 2002 Isolation, characterization and expression of the human factor in the germline alpha (FIGLA) gene in ovarian follicles and oocytes Mol Hum Reprod 8 1087 1095 1:CAS:528:DC%2BD38XpsFOntL4%3D 10.1093/molehr/8.12.1087 12468641 (Pubitemid 36032846)
21. J Infante E Rodriguez-Rodriguez I Mateo J Llorca JL Vazquez-Higuera J Berciano O Combarros 2010 Gene-gene interaction between heme oxygenase-1 and liver X receptor-beta and Alzheimer's disease risk Neurobiol Aging 31 710 714 10.1016/j.neurobiolaging.2008.05.025 1:CAS:528:DC%2BC3cXhvFGgt74%3D 10.1016/j.neurobiolaging.2008.05.025 18597895
22. M Kaare S Seitsonen I Jarvela S Meri H Laivuori 2008 Complement factor H variant Y402H is not a risk factor for preeclampsia in the Finnish population Hypertens Pregnancy 27 328 336 10.1080/10641950801955691 1:CAS:528: DC%2BD1cXhtlKrt77K 10.1080/10641950801955691 19003634
23. RJ Klein C Zeiss EY Chew JY Tsai RS Sackler C Haynes AK Henning JP SanGiovanni SM Mane ST Mayne MB Bracken FL Ferris J Ott C Barnstable J Hoh 2005 Complement factor H polymorphism in age-related macular degeneration Science 308 385 389 10.1126/science.1109557 1:CAS:528:DC%2BD2MXjtFOntLs%3D 10.1126/science.1109557 15761122 (Pubitemid 40530070)
24. N Kriegeskorte WK Simmons PS Bellgowan CI Baker 2009 Circular analysis in systems neuroscience: the dangers of double dipping Nat Neurosci 12 535 540 10.1038/nn.2303 1:CAS:528:DC%2BD1MXltValt7g%3D 10.1038/nn.2303 19396166
25. N Kriegeskorte MA Lindquist TE Nichols RA Poldrack E Vul 2010 Everything you never wanted to know about circular analysis, but were afraid to ask J Cereb Blood Flow Metab 30 1551 1557 10.1038/jcbfm.2010.86 10.1038/jcbfm.2010.86 20571517
26. KY Lain JM Roberts 2002 Contemporary concepts of the pathogenesis and management of preeclampsia JAMA 287 3183 3186 10.1001/jama.287.24.3183 12076198
27. L Liang SM Soyal J Dean 1997 FIGalpha, a germ cell specific transcription factor involved in the coordinate expression of the zona pellucida genes Development 124 4939 4947 1:CAS:528:DyaK1cXjtV2jsA%3D%3D 9362457
28. Løset M, Mundal SB, Johnson MP, Fenstad MH, Freed KA, L. B, Blangero J, Moses EK, Austgulen R (2010) A transcriptional profile of the decidua in preeclampsia. AJOG. doi: 10.1016/j.ajog.2010.08.043
29. S Ma Q Gong HJ Bohnert 2007 An Arabidopsis gene network based on the graphical Gaussian model Genome Res 17 1614 1625 1:CAS:528:DC%2BD2sXhtlSlu7bP 10.1101/gr.6911207 17921353 (Pubitemid 350074857)
30. R Oksjoki PT Kovanen MO Pentikainen 2003 Role of complement activation in atherosclerosis Curr Opin Lipidol 14 477 482 10.1097/01.mol.0000092627.86399.7b 1:CAS:528:DC%2BD3sXntlyrtLg%3D 10.1097/00041433-200310000-00008 14501586
31. R Opgen-Rhein K Strimmer 2007 From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data BMC Syst Biol 1 37 10.1186/1752-0509-1-37 17683609 (Pubitemid 47505533)
32. CW Redman IL Sargent 2003 Pre-eclampsia, the placenta and the maternal systemic inflammatory response-a review Placenta 24 Suppl A S21 S27 10.1053/plac.2002.0930 12842410 (Pubitemid 37184731)
33. JM Roberts HS Gammill 2005 Preeclampsia: recent insights Hypertension 46 1243 1249 1:CAS:528:DC%2BD2MXht1arsrrE 10.1161/01.HYP.0000188408.49896.c5 16230510 (Pubitemid 43189714)
34. JM Roberts G Pearson J Cutler M Lindheimer 2003 Summary of the NHLBI Working Group on Research on hypertension during pregnancy Hypertension 41 437 445 1:CAS:528:DC%2BD3sXhsV2ks78%3D 10.1161/01.HYP.0000054981.03589.E9 12623940 (Pubitemid 36314613)
35. H Salonen Ros P Lichtenstein L Lipworth S Cnattingius 2000 Genetic effects on the liability of developing pre-eclampsia and gestational hypertension Am J Med Genet 91 256 260 1:STN:280:DC%2BD3c3ivFCjsA%3D%3D 10.1002/(SICI)1096-8628(20000410)91:4<256::AID-AJMG3>3.0.CO;2-T 10766979 (Pubitemid 30191247)
36. J Schafer K Strimmer 2005 An empirical Bayes approach to inferring large-scale gene association networks Bioinformatics 21 754 764 10.1093/bioinformatics/bti062 15479708 (Pubitemid 40439411)
37. Schafer J, Strimmer K (2005b) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol 4: Article32
38. S Seitsonen S Lemmela J Holopainen P Tommila P Ranta A Kotamies J Moilanen T Palosaari K Kaarniranta S Meri I Immonen I Jarvela 2006 Analysis of variants in the complement factor H, the elongation of very long chain fatty acids-like 4 and the hemicentin 1 genes of age-related macular degeneration in the Finnish population Mol Vis 12 796 801 1:CAS:528:DC%2BD28XovVKnurc%3D 16885922
39. SP Seitsonen P Onkamo G Peng M Xiong PV Tommila PH Ranta JM Holopainen JA Moilanen T Palosaari K Kaarniranta S Meri IR Immonen IE Jarvela 2008 Multifactor effects and evidence of potential interaction between complement factor H Y402H and LOC387715 A69S in age-related macular degeneration PLoS ONE 3 e3833 10.1371/journal.pone.0003833 19048105
40. K Strimmer 2008 A unified approach to false discovery rate estimation BMC Bioinformatics 9 303 10.1186/1471-2105-9-303 10.1186/1471-2105-9-303 18613966 (Pubitemid 352025239)
41. Z Szolnoki A Maasz L Magyari K Horvatovich B Farago A Kondacs A Bodor F Hadarits P Orosz A Ille B Melegh 2009 Galectin-2 3279TT variant protects against the lymphotoxin-alpha 252GG genotype associated ischaemic stroke Clin Neurol Neurosurg 111 227 230 10.1016/j.clineuro.2008.09.027 10.1016/j.clineuro.2008.09. 027 19013708
42. VD Winn R Haimov-Kochman AC Paquet YJ Yang MS Madhusudhan M Gormley KT Feng DA Bernlohr S McDonagh L Pereira A Sali SJ Fisher 2007 Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term Endocrinology 148 1059 1079 en.2006-0683[pii]10.1210/en. 2006-0683 1:CAS:528:DC%2BD2sXitlWns7w%3D 10.1210/en.2006-0683 17170095
43. VD Winn M Gormley AC Paquet K Kjaer-Sorensen A Kramer KK Rumer R Haimov-Kochman RF Yeh MT Overgaard A Varki C Oxvig SJ Fisher 2009 Severe preeclampsia-related changes in gene expression at the maternal-fetal interface include sialic acid-binding immunoglobulin-like lectin-6 and pappalysin-2 Endocrinology 150 452 462 1:CAS:528:DC%2BD1MXmt1ejtw%3D%3D 10.1210/en.2008-0990 18818296
44. AG Witlin BM Sibai 1997 Hypertension in pregnancy: current concepts of preeclampsia Annu Rev Med 48 115 127 1:CAS:528:DyaK2sXhtFKrurY%3D 10.1146/annurev.med.48.1.115 9046950 (Pubitemid 27101819)
45. H Zhao ZJ Chen Y Qin Y Shi S Wang Y Choi JL Simpson A Rajkovic 2008 Transcription factor FIGLA is mutated in patients with premature ovarian failure Am J Hum Genet 82 1342 1348 1:CAS:528:DC%2BD1cXntlWqs7o%3D 10.1016/j.ajhg.2008. 04.018 18499083