Yang F, Zhai Z, Luo X, Luo G, Zhuang L, Zhang Y, Li Y, Sun E, He Y. Bioinformatics identification of key candidate genes and pathways associated with systemic lupus erythematosus. Clin Rheumatol. 2019;39:425–34.
Javinani A, Ashraf-Ganjouei A, Aslani S, Jamshidi A, Mahmoudi M. Exploring the etiopathogenesis of systemic lupus erythematosus: a genetic perspective. Immunogenetics. 2019;71:283–97.
Article
Google Scholar
Helmick CG, Felson DT, Lawrence RC, Gabriel S, Hirsch R, Kwoh CK, Liang MH, Kremers HM, Mayes MD, Merkel PA, et al. Estimates of the prevalence of arthritis and other rheumatic conditions in the United States. Part I. Arthritis Rheum. 2008;58:15–25.
Article
Google Scholar
Garris C, Shah M, Farrelly E. The prevalence and burden of systemic lupus erythematosus in a medicare population: retrospective analysis of medicare claims. Cost Eff Resour Alloc. 2015;13.
Meas R, Burak MJ, Sweasy JB. DNA repair and systemic lupus erythematosus. DNA Repair (Amst). 2017;56:174–82.
Article
CAS
Google Scholar
Zharkova O, Celhar T, Cravens PD, Satterthwaite AB, Fairhurst AM, Davis LS. Pathways leading to an immunological disease: systemic lupus erythematosus. Rheumatology (Oxford). 2017;56:i55–66.
Article
CAS
Google Scholar
Tsokos GC, Lo MS, Reis PC, Sullivan KE. New insights into the immunopathogenesis of systemic lupus erythematosus. Nat Rev Rheumatol. 2016;12:716–30.
Article
CAS
Google Scholar
Wardemann H, Yurasov S, Schaefer A, Young JW, Meffre E, Nussenzweig MC. Predominant autoantibody production by early human B cell precursors. Science (80-. ). 2003;301:1374–7.
Article
CAS
Google Scholar
Swanson CL, Wilson TJ, Strauch P, Colonna M, Pelanda R, Torres RM. Type I IFN enhances follicular B cell contribution to the T cell-independent antibody response. J Exp Med. 2010;207:1485–500.
Article
CAS
Google Scholar
Xu HC, Grusdat M, Pandyra AA, Polz R, Huang J, Sharma P, Deenen R, Köhrer K, Rahbar R, Diefenbach A, et al. Type I interferon protects antiviral CD8+ T cells from NK cell cytotoxicity. Immunity. 2014;40:949–60.
Article
CAS
Google Scholar
Katsuyama T, Tsokos GC, Moulton VR. Aberrant T cell signaling and subsets in systemic lupus erythematosus. Front Immunol. 2018;9:1–15.
Li Y, Higgs RE, Hoffman RW, Dow ER, Liu X, Petri M, Wallace DJ, Dörner T, Eastwood BJ, Miller BB, et al. A Bayesian gene network reveals insight into the JAK-STAT pathway in systemic lupus erythematosus. PLoS One. 2019;14:1-19.
Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics. 2004;20:3594–603.
Article
CAS
Google Scholar
Gendelman R, Xing H, Mirzoeva OK, Sarde P, Curtis C, Feiler HS, McDonagh P, Gray JW, Khalil I, Korn WM. Bayesian network inference modeling identifies TRIB1 as a novel regulator of cell-cycle progression and survival in cancer cells. Cancer Res. 2017;77:1575–85.
Article
CAS
Google Scholar
Luo, Y.; El Naqa, I.; McShan, D.L.; Ray, D.; Lohse, I.; Matuszak, M.M.; Owen, D.; Jolly, S.; Lawrence, T.S.; Kong, F.-M. (Spring); et al. Unraveling biophysical interactions of radiation pneumonitis in non-small-cell lung cancer via Bayesian network analysis. Radiother.Oncol. 2017, 123, 85–92.
Agrahari R, Foroushani A, Docking TR, Chang L, Duns G, Hudoba M, Karsan A, Zare H. Applications of Bayesian network models in predicting types of hematological malignancies. Sci Rep. 2018;8:6951.
Article
Google Scholar
Ramos J, Das J, Felty Q, Yoo C, Poppiti R, Murrell D, Foster PJ, Roy D. NRF1 motif sequence-enriched genes involved in ER/PR −ve HER2 +ve breast cancer signaling pathways. Breast Cancer Res Treat. 2018;172:469–85.
Article
CAS
Google Scholar
Maleknia, S.; Sharifi-Zarchi, A.; Tabar, V.R.; Namazi, M.; Kavousi, K. BNrich: a Bayesian network approach to the pathway enrichment analysis. bioRxiv 2020, 2020.01.13.905448.
Hamid JS, Hu P, Roslin NM, Ling V, Greenwood CMT, Beyene J. Data integration in genetics and genomics: methods and challenges. Hum Genomics Proteomics. 2009;1:1-13.
Larsen MJ, Thomassen M, Tan Q, Sørensen KP, Kruse TA. Microarray-based RNA profiling of breast cancer: batch effect removal improves cross-platform consistency. Biomed Res Int. 2014;2014:1-11.
Irigoyen A, Jimenez-Luna C, Benavides M, Caba O, Gallego J, Ortuño FM, Guillen-Ponce C, Rojas I, Aranda E, Torres C, et al. Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers. PLoS One. 2018;13:1-16.
Taminau J, Lazar C, Meganck S, Nowé A. Comparison of merging and meta-analysis as alternative approaches for integrative gene expression analysis. ISRN Bioinforma. 2014;2014:1–7.
Article
Google Scholar
Walsh C, Hu P, Batt J, Santos C. Microarray meta-analysis and cross-platform normalization: integrative genomics for robust biomarker discovery. Microarrays. 2015;4:389–406.
Article
Google Scholar
Zhang X, Yu D, Zou G, Liang H. Optimal model averaging estimation for generalized linear models and generalized linear mixed-effects models. J Am Stat Assoc. 2016;111:1775–90.
Article
CAS
Google Scholar
Lee HM, Sugino H, Aoki C, Nishimoto N. Underexpression of mitochondrial-DNA encoded ATP synthesis-related genes and DNA repair genes in systemic lupus erythematosus. Arthritis Res. Ther. 2011;13:R63.
Article
CAS
Google Scholar
Lee HM, Mima T, Sugino H, Aoki C, Adachi Y, Yoshio-Hoshino N, Matsubara K, Nishimoto N. Interactions among type I and type II interferon, tumor necrosis factor, and β-estradiol in the regulation of immune response-related gene expressions in systemic lupus erythematosus. Arthritis Res Ther. 2009;11:R1.
Article
Google Scholar
Kennedy WP, Maciuca R, Wolslegel K, Tew W, Abbas AR, Chaivorapol C, Morimoto A, McBride JM, Brunetta P, Richardson BC, et al. Association of the interferon signature metric with serological disease manifestations but not global activity scores in multiple cohorts of patients with SLE. Lupus Sci Med. 2015;2:1-11.
yun lian Whole genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus Available online: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82221 (accessed on Apr 15, 2018).
Zollars E, Courtney SM, Wolf BJ, Allaire N, Ranger A, Hardiman G, Petri M. Clinical application of a modular genomics technique in systemic lupus erythematosus: Progress towards precision medicine. Int J Genomics. 2016;2016:1-7.
Toro-Domínguez D, Martorell-Marugán J, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME. Stratification of systemic lupus erythematosus patients into three groups of disease activity progression according to longitudinal gene expression. Arthritis Rheumatol. 2018;70:2025–35.
Article
Google Scholar
Petri M, Fu W, Ranger A, Allaire N, Cullen P, Magder LS, Zhang Y. Association between changes in gene signatures expression and disease activity among patients with systemic lupus erythematosus. BMC Med Genet. 2019;12:1-19.
Jiang SH, Athanasopoulos V, Ellyard JI, Chuah A, Cappello J, Cook A, Prabhu SB, Cardenas J, Gu J, Stanley M, et al. Functional rare and low frequency variants in BLK and BANK1 contribute to human lupus. Nat Commun. 2019;10:1-12.
Ritchie ME, Phipson B, Wu DI, Hu Y, Law CW, Shi W, Smyth GK. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
Article
Google Scholar
Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The SVA package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28:882–3.
Article
CAS
Google Scholar
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353–61.
Article
CAS
Google Scholar
Andrade JM, Estévez-Pérez MG. Statistical comparison of the slopes of two regression lines: a tutorial. Anal Chim Acta. 2014;838:1–12.
Article
CAS
Google Scholar
Wasserman, L. All of statistics: a concise course in statistical inference. In The American Statistician; 2004; Vol. 59, pp. 161–163&216–217 ISBN 0387402721.
Wang J, Taaffe MR. Multivariate mixtures of normal distributions: properties, random vector generation, fitting, and as models of market daily changes. INFORMS J Comput. 2015;27:193–203.
Article
Google Scholar
Asadipour M, Hassan-Zadeh V, Aryaeian N, Shahram F, Mahmoudi M. Histone variants expression in peripheral blood mononuclear cells of patients with rheumatoid arthritis. Int J Rheum Dis. 2018;21:1831–7.
Article
CAS
Google Scholar
Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, Graham RR, Ortmann W, Criswell LA, Yeo GW, et al. The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science (80-. ). 2015;350:455–9.
Article
CAS
Google Scholar
Kamiyama R, Yoshimi R, Takeno M, Iribe Y, Tsukahara T, Kishimoto D, Kunishita Y, Sugiyama Y, Tsuchida N, Nakano H, et al. Dysfunction of TRIM21 in interferon signature of systemic lupus erythematosus. Mod Rheumatol. 2018;28:993–1003.
Article
CAS
Google Scholar
Espinosa A, Dardalhon V, Brauner S, Ambrosi A, Higgs R, Quintana FJ, Sjöstrand M, Eloranta ML, Gabhann JN, Winqvist O, et al. Loss of the lupus autoantigen Ro52/Trim21 induces tissue inflammation and systemic autoimmunity by disregulating the IL-23-Th17 pathway. J Exp Med. 2009;206:1661–71.
Article
CAS
Google Scholar
Shimada-Sugimoto M, Otowa T, Miyagawa T, Khor SS, Kashiwase K, Sugaya N, Kawamura Y, Umekage T, Kojima H, Saji H, et al. Immune-related pathways including HLA-DRB1*13:02 are associated with panic disorder. Brain Behav Immun. 2015;46:96–103.
Article
CAS
Google Scholar
Kunishita Y, Yoshimi R, Kamiyama R, Kishimoto D, Yoshida K, Hashimoto E, Komiya T, Sakurai N, Sugiyama Y, Kirino Y, et al. TRIM21 dysfunction enhances aberrant B-cell differentiation in autoimmune pathogenesis. Front Immunol. 2020;11.
Hachicha, H.; Kammoun, A.; Mahfoudh, N.; Marzouk, S.; Feki, S.; Fakhfakh, R.; Fourati, H.; Haddouk, S.; Frikha, F.; Gaddour, L.; et al. Human leukocyte antigens-DRB1*03 is associated with systemic lupus erythematosus and anti-SSB production in South Tunisia. Int. J. Health Sci. (Qassim). 12, 21–27.
De Leeuw, K.; Kallenberg, C.G.M. Antibodies against c1q; 2018; ISBN 9780323479271.
Google Scholar
Quiroz EN, Chavez-Estrada V, Macias-Ochoa K, Ayala-Navarro MF, Flores-Aguilar AS, Morales-Navarrete F, Lopez F, de la C, Escorcia LG, Musso CG, Martinez GA, et al. Epigenetic mechanisms and posttranslational modifications in systemic lupus erythematosus. Int. J Mol Sci. 2019;20:1-20.
Webber D, Cao J, Dominguez D, Gladman DD, Levy DM, Ng L, Paterson AD, Touma Z, Urowitz MB, Wither JE, et al. Association of systemic lupus erythematosus (SLE) genetic susceptibility loci with lupus nephritis in childhood-onset and adult-onset SLE. Rheumatol. (United Kingdom). 2020;59:90–8.
Google Scholar
Jacob N, Stohl W. Cytokine disturbances in systemic lupus erythematosus. Arthritis Res. Ther. 2011;13.
Karnell JL, Rieder SA, Ettinger R, Kolbeck R. Targeting the CD40-CD40L pathway in autoimmune diseases: Humoral immunity and beyond. Adv Drug Deliv Rev. 2019;141:92–103.
Article
CAS
Google Scholar
Macedo ACL, Isaac L. Systemic lupus erythematosus and deficiencies of early components of the complement classical pathway. Front Immunol. 2016;7:1-7.
Haynes WA, Haddon DJ, Diep VK, Khatri A, Bongen E, Yiu G, Balboni I, Bolen CR, Mao R, Utz PJ, et al. Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus. JCI Insight. 2020;5(4):1-20.
Jakez-Ocampo J, Paulín-Vera CM, Gómez-Martín D, Lima G, Vargas-Rojas MI, Llorente L, Rivadeneyra-Espinoza L, Pérez-Romano B, Calva-Cevenini G, Ruiz-Argüelles A, et al. Vß T cell receptor (TCR) genes in circulating cells of patients with systemic lupus erythematosus and their healthy relatives. Gac Med Mex. 2018;154:74–9.
PubMed
Google Scholar
Ma K, Du W, Wang X, Yuan S, Cai X, Liu D, Li J, Lu L. Multiple functions of B cells in the pathogenesis of systemic lupus erythematosus. Int J. Mol. Sci. 2019;20:1-19.
Sharabi A, Tsokos GC. T cell metabolism: new insights in systemic lupus erythematosus pathogenesis and therapy. Nat Rev Rheumatol. 2020;16:100–12.
Article
CAS
Google Scholar
Matsuo T, Hashimoto M, Sakaguchi S, Sakaguchi N, Ito Y, Hikida M, Tsuruyama T, Sakai K, Yokoi H, Shirakashi M, et al. Strain-specific manifestation of lupus-like systemic autoimmunity caused by Zap70 mutation. J Immunol. 2019;202:3161–72.
Article
CAS
Google Scholar
Julià A, López-Longo FJ, Pérez Venegas JJ, Bonàs-Guarch S, Olivé À, Andreu JL, Aguirre-Zamorano MÁ, Vela P, Nolla JM, de la Fuente JLM, et al. Genome-wide association study meta-analysis identifies five new loci for systemic lupus erythematosus. Arthritis Res. Ther. 2018;20:1-10.
He J, Ma J, Ren B, Liu A. Advances in systemic lupus erythematosus pathogenesis via mTOR signaling pathway. Semin Arthritis Rheum.
Beşliu AN, Pistol G, Marica CM, Bǎnicǎ LM, Chiţonu C, Ionescu R, Tǎnǎseanu C, Tamsulea I, Matache C, Stefǎnescu M. PI3K/Akt signaling in peripheral T lymphocytes from systemic lupus erythematosus patients. Roum Arch Microbiol Immunol. 2009;68:69–79.
PubMed
Google Scholar
Wilbe M, Kozyrev SV, Farias FHG, Bremer HD, Hedlund A, Pielberg GR, Seppälä EH, Gustafson U, Lohi H, Carlborg Ö, et al. Multiple changes of gene expression and function reveal genomic and phenotypic complexity in SLE-like disease. PLoS Genet. 2015;11:1-27.
Sui W, Hou X, Che W, Yang M, Dai Y. The applied basic research of systemic lupus erythematosus based on the biological omics. Genes Immun. 2013;14:133–46.