Erratum: Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain (Mol Neurodegener (2016) 11 (31) DOI: 10.1186/s13024-016-0095-2);Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain

Molecular Neurodegeneration

Volumn 11, Issue 1, 2016, Pages

  Jaeger, Philipp A ^a,b,c   Lucin, Kurt M ^a,p   Britschgi, Markus ^a,q   Vardarajan, Badri ^d   Huang, Ruo Pan ^e,f   Kirby, Elizabeth D ^a   Abbey, Rachelle ^a   Boeve, Bradley F ^g   Boxer, Adam L ^h   Farrer, Lindsay A ^d   Finch, Nicole ⁱ   Graff Radford, Neill R ^j   Head, Elizabeth ^k   Hofree, Matan ^l   Huang, Ruochun ^e,f   Johns, Hudson ^a   Karydas, Anna ^h   Knopman, David S ^g   Loboda, Andrey ^m   Masliah, Eliezer ⁿ   Narasimhan, Ramya ^a   Petersen, Ronald C ^g   Podtelezhnikov, Alexei ^m   Pradhan, Suraj ^a   Rademakers, Rosa ⁱ   Sun, Chung Huan ^a   Younkin, Steven G ⁱ   Miller, Bruce L ^h   Ideker, Trey ^c   Wyss Coray, Tony ^a,o   more..

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e RayBiotech ^*  (China)

^f RayBiotech   (United States)

^g MAYO CLINIC   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ MAYO GRADUATE SCHOOL   (United States)

^j MAYO CLINIC   (United States)

^k UNIVERSITY OF KENTUCKY   (United States)

^l UNIVERSITY OF CALIFORNIA   (United States)

^m MERCK RESEARCH LABORATORIES   (United States)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o VA PALO ALTO HEALTH CARE SYSTEM   (United States)

^p EASTERN CONNECTICUT STATE UNIVERSITY   (United States)

^q F HOFFMANN LA ROCHE LTD   (Switzerland)

more..

Author keywords

[No Author keywords available]

Indexed keywords

GROWTH DIFFERENTIATION FACTOR 3; AMYLOID BETA PROTEIN; AMYLOID PRECURSOR PROTEIN;

ACCESS TO INFORMATION; ALZHEIMER DISEASE; ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BLOOD SAMPLING; CONTROLLED STUDY; FEMALE; GENOME ANALYSIS; HUMAN; HUMAN CELL; HUMAN TISSUE; INTRACELLULAR SIGNALING; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; MOLECULAR MODEL; MOLECULAR PROBE; MOUSE; NONHUMAN; PROTEIN DETERMINATION; PROTEOMICS; TRANSCRIPTOMICS; BRAIN; METABOLISM; NERVE CELL NETWORK; PHYSIOLOGY; SIGNAL TRANSDUCTION;

ALZHEIMER DISEASE; AMYLOID BETA-PEPTIDES; AMYLOID BETA-PROTEIN PRECURSOR; BRAIN; HUMANS; NERVE NET; PROTEOMICS; SIGNAL TRANSDUCTION;

EID: 84969256193     PISSN: None     EISSN: 17501326     Source Type: Journal    
DOI: 10.1186/s13024-016-0105-4     Document Type: Erratum

References (87)

1. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol. 2006;24:971-83.
2. Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nat Biotechnol. 2010;28:695-709.
3. Kiddle SJ, Sattlecker M, Proitsi P, Simmons A, Westman E, Bazenet C, Nelson SK, Williams S, Hodges A, Johnston C, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Newhouse S, Lovestone S, Dobson RJB. Candidate blood proteome markers of Alzheimer's disease onset and progression: a systematic review and replication study. J Alzheimers Dis. 2014;38:515-31.
4. Jaeger PA, Villeda SA, Berdnik D, Britschgi M, Wyss-Coray T. Focused plasma proteomics for the study of brain aging and neurodegeneration. In: Coppola G, editor. The OMICS: Applications in Neuroscience. New York: Oxford Univ. Press; 2014. p. 183-91.
5. Snowden J, Neary D, Mann D. Frontotemporal lobar degeneration: clinical and pathological relationships. Acta Neuropathol. 2007;114:31-8.
6. Hodges JR, Mitchell J, Dawson K, Spillantini MG, Xuereb JH, McMonagle P, Nestor PJ, Patterson K. Semantic dementia: demography, familial factors and survival in a consecutive series of 100 cases. Brain. 2010;133:300-6.
7. Miller ZA, Rankin KP, Graff-Radford NR, Takada LT, Sturm VE, Cleveland CM, Criswell LA, Jaeger PA, Stan T, Heggeli KA, Hsu SC, Karydas A, Khan BK, Grinberg LT, Gorno-Tempini M-L, Boxer AL, Rosen HJ, Kramer JH, Coppola G, Geschwind DH, Rademakers R, Seeley WW, Wyss-Coray T, Miller BL. TDP-43 frontotemporal lobar degeneration and autoimmune disease. J Neurol Neurosurg Psychiatr. 2013;84:956-62.
8. La Joie R, Landeau B, Perrotin A, Bejanin A, Egret S, Pélerin A, Mézenge F, Belliard S, de La Sayette V, Eustache F, Desgranges B, Chételat G. Intrinsic connectivity identifies the hippocampus as a main crossroad between Alzheimer'sand semantic dementia-targeted networks. Neuron. 2014;81:1417-28.
9. Jaeger PA. Cytokine and Leukocyte Profiling Reveal Pro-Inflammatory and Autoimmune Features in Frontotemporal Dementia Patients. http://dx.doi.org/10.1101/049791.
10. Folstein MF, Folstein SE, McHugh PR. "Mini-mental state." A practical method for grading the cognitive state of patients for the clinician. J Psychiatr Res. 1975;12:189-98.
11. de La Fuente A. From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases. Trends Genet. 2010;26:326-33.
12. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998;95:14863-8.
13. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.
14. Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37:1-13.
15. Lewis RD, Perry MJ, Guschina IA, Jackson CL, Morgan BP, Hughes TR. CD55 deficiency protects against atherosclerosis in ApoE-deficient mice via C3a modulation of lipid metabolism. Am J Pathol. 2011;179:1601-7.
16. Wada H, Ura S, Kitaoka S, Satoh-Asahara N, Horie T, Ono K, Takaya T, Takanabe-Mori R, Akao M, Abe M, Morimoto T, Murayama T, Yokode M, Fujita M, Shimatsu A, Hasegawa K. Distinct characteristics of circulating vascular endothelial growth factor-a and C levels in human subjects. PLoS ONE. 2011;6, e29351.
17. Eickelberg O, Pansky A, Koehler E, Bihl M, Tamm M, Hildebrand P, Perruchoud AP, Kashgarian M, Roth M. Molecular mechanisms of TGF-(beta) antagonism by interferon (gamma) and cyclosporine A in lung fibroblasts. FASEB J. 2001;15:797-806.
18. Strickertsson JAB, Døssing KBV, Aabakke AJM, Nilsson H-O, Hansen TVO, Knigge U, Kjær A, Wadström T, Friis-Hansen L. Interferon-γ inhibits ghrelin expression and secretion via a somatostatin-mediated mechanism. World J Gastroenterol. 2011;17:3117-25.
19. Shibanuma M, Mashimo J, Mita A, Kuroki T, Nose K. Cloning from a mouse osteoblastic cell line of a set of transforming-growth-factor-beta 1-regulated genes, one of which seems to encode a follistatin-related polypeptide. Eur J Biochem. 1993;217:13-9.
20. Britschgi M, Rufibach K, Huang SLB, Clark CM, Kaye JA, Li G, Peskind ER, Quinn JF, Galasko DR, Wyss-Coray T. Modeling of pathological traits in Alzheimer's disease based on systemic extracellular signaling proteome. Mol Cell Proteomics. 2011;10:M111. 008862.
21. Ray S, Britschgi M, Herbert C, Takeda-Uchimura Y, Boxer A, Blennow K, Friedman LF, Galasko DR, Jutel M, Karydas A, Kaye JA, Leszek J, Miller BL, Minthon L, Quinn JF, Rabinovici GD, Robinson WH, Sabbagh MN, So YT, Sparks DL, Tabaton M, Tinklenberg J, Yesavage JA, Tibshirani R, Wyss-Coray T. Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med. 2007;13:1359-62.
22. Zhang B, Gaiteri C, Bodea L-G, Wang Z, McElwee J, Podtelezhnikov AA, Zhang C, Xie T, Tran L, Dobrin R, Fluder E, Clurman B, Melquist S, Narayanan M, Suver C, Shah H, Mahajan M, Gillis T, Mysore J, MacDonald ME, Lamb JR, Bennett DA, Molony C, Stone DJ, Gudnason V, Myers AJ, Schadt EE, Neumann H, Zhu J, Emilsson V. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell. 2013;153:707-20.
23. Naj AC, Jun G, Beecham GW, Wang L-S, Vardarajan BN, Buros J, Gallins PJ, Buxbaum JD, Jarvik GP, Crane PK, Larson EB, Bird TD, Boeve BF, Graff-Radford NR, De Jager PL, Evans D, Schneider JA, Carrasquillo MM, Ertekin-Taner N, Younkin SG, Cruchaga C, Kauwe JSK, Nowotny P, Kramer P, Hardy J, Huentelman MJ, Myers AJ, Barmada MM, Demirci FY, Baldwin CT, et al. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet. 2011.
24. Podtelezhnikov AA, Tanis KQ, Nebozhyn M, Ray WJ, Stone DJ, Loboda AP. Molecular insights into the pathogenesis of Alzheimer's disease and its relationship to normal aging. PLoS ONE. 2011;6, e29610.
25. Wyss-Coray T, Lin C, Yan F, Yu GQ, Rohde M, McConlogue L, Masliah E, Mucke L. TGF-beta1 promotes microglial amyloid-beta clearance and reduces plaque burden in transgenic mice. Nat Med. 2001;7:612-8.
26. Town T, Laouar Y, Pittenger C, Mori T, Szekely CA, Tan J, Duman RS, Flavell RA. Blocking TGF-β-Smad2/3 innate immune signaling mitigates Alzheimer-like pathology. Nat Med. 2008.
27. Burke RM, Norman TA, Haydar TF, Slack BE, Leeman SE, Blusztajn JK, Mellott TJ. BMP9 ameliorates amyloidosis and the cholinergic defect in a mouse model of Alzheimer's disease. Proc Natl Acad Sci U S A. 2013;110:19567-72.
28. Hexige S, Guo J, Ma L, Sun Y, Liu X, Ma L, Yan X, Li Z, Yu L. Expression pattern of growth/differentiation factor 3 in human and murine cerebral cortex, hippocampus as well as cerebellum. Neurosci Lett. 2005;389:83-7.
29. Levine AJ, Brivanlou AH. GDF3, a BMP inhibitor, regulates cell fate in stem cells and early embryos. Development. 2006;133:209-16.
30. Levine AJ, Brivanlou AH. GDF3 at the crossroads of TGF-beta signaling. Cell Cycle. 2006;5:1069-73.
31. Tykwinska K, Lauster R, Knaus P, Rosowski M. Growth and differentiation factor 3 induces expression of genes related to differentiation in a model of cancer stem cells and protects them from retinoic acid-induced apoptosis. PLoS ONE. 2013;8, e70612.
32. Calloni R, Cordero EAA, Henriques JAP, Bonatto D. Reviewing and updating the major molecular markers for stem cells. Stem Cells Dev. 2013;22:1455-76.
33. Li Q, Liu X, Wu Y, An J, Hexige S, Ling Y, Zhang M, Yang X, Yu L. The conditioned medium from a stable human GDF3-expressing CHO cell line, induces the differentiation of PC12 cells. Mol Cell Biochem. 2011;359:115-23.
34. Villeda SA, Luo J, Mosher KI, Zou B, Britschgi M, Bieri G, Stan TM, Fainberg N, Ding Z, Eggel A, Lucin KM, Czirr E, Park J-S, Couillard-Després S, Aigner L, Li G, Peskind ER, Kaye JA, Quinn JF, Galasko DR, Xie XS, Rando TA, Wyss-Coray T. The ageing systemic milieu negatively regulates neurogenesis and cognitive function. Nature. 2011;477:90-4.
35. Lu T, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang T-H, Kim H-M, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA. REST and stress resistance in ageing and Alzheimer's disease. Nature. 2014;507:448-54.
36. Kidder BL, Yang J, Palmer S. Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells. PLoS ONE. 2008;3, e3932.
37. Spalding KL, Bergmann O, Alkass K, Bernard S, Salehpour M, Huttner HB, Boström E, Westerlund I, Vial C, Buchholz BA, Possnert G, Mash DC, Druid H, Frisén J. Dynamics of hippocampal neurogenesis in adult humans. Cell. 2013;153:1219-27.
38. Tsai K-J, Tsai Y-C, Shen C-KJ. G-CSF rescues the memory impairment of animal models of Alzheimer's disease. J Exp Med. 2007;204:1273-80.
39. Ma Q-H, Futagawa T, Yang W-L, Jiang X-D, Zeng L, Takeda Y, Xu R-X, Bagnard D, Schachner M, Furley AJ, Karagogeos D, Watanabe K, Dawe GS, Xiao Z-C. A TAG1-APP signalling pathway through Fe65 negatively modulates neurogenesis. Nat Cell Biol. 2008;10:283-94.
40. Sattlecker M, Kiddle SJ, Newhouse S, Proitsi P, Nelson S, Williams S, Johnston C, Killick R, Simmons A, Westman E, Hodges A, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Lovestone S, Dobson RJB, Consortium TA. Alzheimer's disease biomarker discovery using SOMAscan multiplexed protein technology. Alzheimers Dement. 2014;10:724-34.
41. Zhao X, Lejnine S, Spond J, Zhang C, Ramaraj TC, Holder DJ, Dai H, Weiner R, Laterza OF. A candidate plasma protein classifier to identify Alzheimer's disease. J Alzheimers Dis. 2015;43:549-63.
42. Wang J, Li M, Deng Y, Pan Y. Recent advances in clustering methods for protein interaction networks. BMC Genomics. 2010;11:S10.
43. Dalton L, Ballarin V, Brun M. Clustering algorithms: on learning, validation, performance, and applications to genomics. Curr Genomics. 2009;10:430-45.
44. Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I. Biases in the experimental annotations of protein function and their effect on Our understanding of protein function space. PLoS Comput Biol. 2013;9, e1003063.
45. Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 2013;42:D1269-74.
46. Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics. 2014;30:i34-42.
47. O'Bryant SE, Xiao G, Barber R, Reisch J, Doody R, Fairchild T, Adams P, Waring S, Diaz-Arrastia R, for the Texas Alzheimer's Research Consortium. A serum protein-based algorithm for the detection of Alzheimer disease. Arch Neurol. 2010;67:1077-81.
48. Hu WT, Chen-Plotkin A, Arnold SE, Grossman M, Clark CM, Shaw LM, Mccluskey L, Elman L, Karlawish J, Hurtig HI, Siderowf A, Lee VM-Y, Soares H, Trojanowski JQ. Biomarker discovery for Alzheimer"s disease, frontotemporal lobar degeneration, and Parkinson"s disease. Acta Neuropathol. 2010;120:385-99.
49. Craig-Schapiro R, Kuhn M, Xiong C, Pickering EH, Liu J, Misko TP, Perrin RJ, Bales KR, Soares H, Fagan AM. Multiplexed immunoassay panel identifies novel CSF biomarkers for Alzheimer's disease diagnosis and prognosis. PLoS ONE. 2011;6, e18850.
50. Soares HD, Potter WZ, Pickering E, Kuhn M, Immermann FW, Shera DM, Ferm M, Dean RA, Simon AJ, Swenson F, Siuciak JA, Kaplow J, Thambisetty M, Zagouras P, Koroshetz WJ, Wan HI, Trojanowski JQ, Shaw LM, Biomarkers Consortium Alzheimer's Disease Plasma Proteomics Project. Plasma biomarkers associated with the apolipoprotein E genotype and Alzheimer disease. Arch Neurol. 2012;69:1310-7.
51. Ringman JM, Elashoff D, Geschwind DH, Welsh BT, Gylys KH, Lee C, Cummings JL, Cole GM. Plasma signaling proteins in persons at genetic risk for Alzheimer disease: influence of APOE genotype. Arch Neurol. 2012;69:757-64.
52. Doecke JD, Laws SM, Faux NG, Wilson W, Burnham SC, Lam C-P, Mondal A, Bedo J, Bush AI, Brown B, De Ruyck K, Ellis KA, Fowler C, Gupta VB, Head R, Macaulay SL, Pertile K, Rowe CC, Rembach A, Rodrigues M, Rumble R, Szoeke C, Taddei K, Taddei T, Trounson B, Ames D, Masters CL, Martins RN, Alzheimer's Disease Neuroimaging Initiative, Australian Imaging Biomarker and Lifestyle Research Group. Blood-based protein biomarkers for diagnosis of Alzheimer disease. Arch Neurol. 2012;69:1318-25.
53. Hu WT, Holtzman DM, Fagan AM, Shaw LM, Perrin R, Arnold SE, Grossman M, Xiong C, Craig-Schapiro R, Clark CM, Pickering E, Kuhn M, Chen Y, Van Deerlin VM, Mccluskey L, Elman L, Karlawish J, Chen-Plotkin A, Hurtig HI, Siderowf A, Swenson F, Lee VM-Y, Morris JC, Trojanowski JQ, Soares H, Initi ADN. Plasma multianalyte profiling in mild cognitive impairment and Alzheimer disease. Neurology. 2012;79:897-905.
54. Leung V, Gillis J, Raboud J, Cooper C, Hogg RS, Loutfy MR, Machouf N, Montaner JSG, Rourke SB, Tsoukas C, Klein MB, CANOC Collaboration. Predictors of CD4:CD8 ratio normalization and its effect on health outcomes in the era of combination antiretroviral therapy. PLoS ONE. 2013;8:e77665.
55. Llano DA, Devanarayan V, Simon AJ, ADNI. Evaluation of plasma proteomic data for Alzheimer disease state classification and for the prediction of progression from mild cognitive impairment to Alzheimer disease. Alzheimer Dis Assoc Disord. 2013;27:233-43.
56. Guo L-H, Alexopoulos P, Wagenpfeil S, Kurz A, Perneczky R, Neuroimaging AD. Plasma proteomics for the identification of Alzheimer disease. Alzheimer Dis Assoc Disord. 2013;27:337-42.
57. Burnham SC, Faux NG, Wilson W, Laws SM, Ames D, Bedo J, Bush AI, Doecke JD, Ellis KA, Head R, Jones G, Kiiveri H, Martins RN, Rembach A, Rowe CC, Salvado O, Macaulay SL, Masters CL, Villemagne VL, Initiative ARSDN, Australian Imaging BALSRG. A blood-based predictor for neocortical Ab burden in Alzheimer's disease: results from the AIBL study. Mol Psychiatry. 2013;19:519-26.
58. Delaby C, Gabelle A, Blum D, Schraen-Maschke S, Moulinier A, Boulanghien J, Séverac D, Buée L, Rème T, Lehmann S. Central nervous system and peripheral inflammatory processes in Alzheimer's disease: biomarker profiling approach. Front Neurol. 2015;6:103.
59. Lehallier B, Essioux L, Gayan J, Alexandridis R, Nikolcheva T, Wyss-Coray T, Britschgi M, for the Alzheimer's Disease Neuroimaging Initiative. Combined plasma and cerebrospinal fluid signature for the prediction of midterm progression from mild cognitive impairment to Alzheimer disease. JAMA Neurol. 2015;1.
60. Chiam JTW, Dobson RJB, Kiddle SJ, Sattlecker M. Are blood-based protein biomarkers for Alzheimer's disease also involved in other brain disorders? A systematic review. J Alzheimers Dis. 2015;43:303-14.
61. McKhann GM, Knopman DS, Chertkow H, Hyman BT, Jack Jr CR, Kawas CH, Klunk WE, Koroshetz WJ, Manly JJ, Mayeux R, Mohs RC, Morris JC, Rossor MN, Scheltens P, Carillo MC, Thies B, Weintraub S, Phelps CH. The diagnosis of dementia due to Alzheimer's disease: recommendations from the national institute on aging and the Alzheimer's association workgroup. Alzheimers Dement. 2011;1-7.
62. Gorno-Tempini ML, Hillis AE, Weintraub S, Kertesz A, Mendez M, Cappa SF, Ogar JM, Rohrer JD, Black S, Boeve BF, Manes F, Dronkers NF, Vandenberghe R, Rascovsky K, Patterson K, Miller BL, Knopman DS, Hodges JR, Mesulam MM, Grossman M. Classification of primary progressive aphasia and its variants. Neurology. 2011;76:1006-14.
63. Eisen M, de Hoon M. Cluster 3.0 Manual. 2002. p. 1-34.
64. Storey JD. A direct approach to false discovery rates - Storey - 2002 - Journal of the Royal Statistical Society: Series B. J R Stat Soc Ser B. 2002;64:479-98.
65. Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics. 2010;26:2927-8.
66. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498-504.
67. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res. 2009;37(Database):D674-9.
68. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2010;39(Database):D691-7.
69. Joshi-Tope G. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2004;33(Database issue):D428-32.
70. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2013;42:D472-7.
71. Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 2010;11:R53.
72. Chatr-aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2015;43:D470-8.
73. Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ. iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database. 2010;2010:baq023-3.
74. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G, Consortium GO. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25-9.
75. The Gene Ontology Consortium. Gene ontology consortium: going forward. Nucleic Acids Res. 2015;43:D1049-56.
76. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27-30.
77. Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013;8:1551-66.
78. Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol. 2012;8:565.
79. Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010;26:976-8.
80. Halekoh U, Højsgaard S. The R package geepack for generalized estimating equations. J Stat Softw. 2006.
81. Chen M-H, Yang Q. GWAF: an R package for genome-wide association analyses with family data. Bioinformatics. 2010;26:580-1.
82. Willer CJ, Li Y, Abecasis GR. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics. 2010;26:2190-1.
83. Li J, Ji L. Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity (Edinb). 2005;95:221-7.
84. Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM, AMFS Investigators, Hayward NK, Montgomery GW, Visscher PM, Martin NG, Macgregor S. A versatile gene-based test for genome-wide association studies. Am J Hum Genet. 2010;87:139-45.
85. Babu H, Claasen J-H, Kannan S, Rünker AE, Palmer T, Kempermann G. A protocol for isolation and enriched monolayer cultivation of neural precursor cells from mouse dentate gyrus. Front Neurosci. 2011;5.
86. Gurok U, Steinhoff C, Lipkowitz B, Ropers H-H, Scharff C, Nuber UA. Gene expression changes in the course of neural progenitor cell differentiation. J Neurosci. 2004;24:5982-6002.
87. Castaño Z, Kypta RM. Housekeeping proteins: limitations as references during neuronal differentiation. Open Neurosci J. 2008;2.