Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity

F1000Research

Volumn 5, Issue , 2016, Pages

  Lau, William W ^a   Sparks, Rachel ^b   Tsang, John S ^b   Austin, James ^b   Bansal, Neha ^b   Candia, Julián ^c   Dancy, Ehren ^b   Elkins, Karen L ^d   Faghihi Kashani, Sara ^e   Gomez Rodriguez, Julio ^f   Guedez, Liliana ^g   Guo, Yongjian ^b   Gutierrez, Maria J ^h   Ho, Trung ⁱ   Horai, Reiko ^g   Huh, Sunmee ^j   Iwamura, Chie ^k   Joy, Jaimy ^l   Kang, Ju Gyeong ^m   Kaul, Sunil ^j   Lewandowski, Laura B ⁿ   Liu, Candace ^b   Lu, Yong ^b   Manes, Nathan P ^b   Mattapallil, Mary J ^g   Memon, Sarfraz ^j   Jubayer Rahman, M ^k   Rodrigues, Kameron B ^k   Silva, Bruno ^l   Singh, Amit ^l   St Leger, Anthony J ^g   Tang, Jessica ^m   Thorpe, Abigail ^b   Xie, Hang ^d   Zhao, Yongge ^j   Zimmerman, Ofer ^b   more..

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^e NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^f NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^g NATIONAL EYE INSTITUTE   (United States)

^h JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES   (United States)

^j NATIONAL CANCER INSTITUTE   (United States)

^k NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^l NATIONAL INSTITUTE ON AGING   (United States)

^m NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

ⁿ NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES   (United States)

more..

Author keywords

Autoimmunity; Crowdsourcing; Gene expression; Human andmouse comparison; Meta analysis; Mouse modelsof disease; Public data

Indexed keywords

AUTOIMMUNITY; BIOINFORMATICS; CROWDSOURCING; DATA ANALYSIS; DATA PROCESSING; EFFECT SIZE; GENE EXPRESSION REGULATION; GENETIC DATABASE; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; MEDICAL EDUCATION; MULTIPLE SCLEROSIS; NONHUMAN; NOTE; QUALITY CONTROL; RHEUMATOID ARTHRITIS; SYSTEMIC LUPUS ERYTHEMATOSUS; UPREGULATION;

EID: 85006816750     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.10465.1     Document Type: Note

References (30)

1. Rung J Brazma A: Reuse of public genome-wide gene expression data. Nat Rev Genet. 2013;14(2):89-99. 23269463 10.1038/nrg3394
2. Saez-Rodriguez J Costello JC Friend SH: Crowdsourcing biomedical research: leveraging communities as innovation engines. Nat Rev Genet. 2016;17(8):470-86. 27418159 10.1038/nrg.2016.69
3. Celi LA Lokhandwala S Montgomery R: Datathons and Software to Promote Reproducible Research. J Med Internet Res. 2016;18(8):e230. 27558834 10.2196/jmir.6365 5014984
4. Shah N Guo Y Wendelsdorf KV: A crowdsourcing approach for reusing and meta-analyzing gene expression data. Nat Biotechnol. 2016;34(8):803-6. 27323300 10.1038/nbt.3603
5. Sparks R Lau WW Tsang JS: Expanding the immunology toolbox: embracing public-data reuse and crowdsourcing. Immunity. 2016. 10.1016/j.immuni.2016.12.008
6. Seok J Warren HS Cuenca AG: Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci U S A. 2013;110(9):3507-12. 23401516 10.1073/pnas.1222878110 3587220
7. Webb DR: Animal models of human disease: inflammation. Biochem Pharmacol. 2014;87(1):121-30. 23811309 10.1016/j.bcp.2013.06.014
8. Toro-Domínguez D Carmona-Sáez P Alarcón-Riquelme ME: Shared signatures between rheumatoid arthritis, systemic lupus erythematosus and Sjögren's syndrome uncovered through gene expression meta-analysis. Arthritis Res Ther. 2014;16(6):489. 25466291 10.1186/s13075-014-0489-x 4295333
9. Godec J Tan Y Liberzon A: Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. 2016;44(1):194-206. 26795250 10.1016/j.immuni.2015.12.006
10. Takao K Miyakawa T: Genomic responses in mouse models greatly mimic human inflammatory diseases. Proc Natl Acad Sci U S A. 2015;112(4):1167-72. 25092317 10.1073/pnas.1401965111 4313832
11. Hong F Breitling R McEntee CW: RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics. 2006;22(22):2825-7. 16982708 10.1093/bioinformatics/btl476
12. Yu G Wang LG Han Y: clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284-7. 22455463 10.1089/omi.2011.0118 3339379
13. Yu G He QY: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Mol Biosyst. 2016;12(2):477-9. 26661513 10.1039/c5mb00663e
14. Chen J Bardes EE Aronow BJ: ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 2009;37(Web Server issue):W305-11. 19465376 10.1093/nar/gkp427 2703978
15. Tseng GC Ghosh D Feingold E: Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res. 2012;40(9):3785-99. 22262733 10.1093/nar/gkr1265 3351145
16. Sweeney TE Haynes WA Vallania F: Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res. 2016; pii: gkw797. 27634930 10.1093/nar/gkw797
17. Baechler EC Batliwalla FM Karypis G: Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci U S A. 2003;100(5):2610-5. 12604793 10.1073/pnas.0337679100 151388
18. Bennett L Palucka AK Arce E: Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 2003;197(6):711-23. 12642603 10.1084/jem.20021553 2193846
19. Higgs BW Liu Z White B: Patients with systemic lupus erythematosus, myositis, rheumatoid arthritis and scleroderma share activation of a common type I interferon pathway. Ann Rheum Dis. 2011;70(11):2029-36. 21803750 10.1136/ard.2011.150326
20. Liu Z Bethunaickan R Huang W: Interferon-α accelerates murine systemic lupus erythematosus in a T cell-dependent manner. Arthritis Rheum. 2011;63(1):219-29. 20954185 10.1002/art.30087 3014995
21. Tsokos GC Lo MS Reis PC: New insights into the immunopathogenesis of systemic lupus erythematosus. Nat Rev Rheumatol. 2016;12(12):716-30. 27872476 10.1038/nrrheum.2016.186
22. van Vollenhoven RF: Treatment of rheumatoid arthritis: state of the art 2009. Nat Rev Rheumatol. 2009;5(10):531-41. 19798027 10.1038/nrrheum.2009.182
23. Kyburz D Brentano F Gay S: Mode of action of hydroxychloroquine in RA-evidence of an inhibitory effect on toll-like receptor signaling. Nat Clin Pract Rheumatol. 2006;2(9):458-9. 16951696 10.1038/ncprheum0292
24. Habets KL Huizinga TW Toes RE: Platelets and autoimmunity. Eur J Clin Invest. 2013;43(7):746-57. 23617819 10.1111/eci.12101
25. Boilard E Nigrovic PA Larabee K: Platelets amplify inflammation in arthritis via collagen-dependent microparticle production. Science. 2010;327(5965):580-3. 20110505 10.1126/science.1181928 2927861
26. Boilard E Blanco P Nigrovic PA: Platelets: active players in the pathogenesis of arthritis and SLE. Nat Rev Rheumatol. 2012;8(9):534-42. 22868927 10.1038/nrrheum.2012.118
27. Lau WW Sparks R OMiCC Jamboree Working Group,: Dataset 1 in: Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity. F1000Research. 2016. Data Source
28. Lau WW Sparks R OMiCC Jamboree Working Group,: Dataset 2 in: Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity. F1000Research. 2016. Data Source
29. Lau WW Sparks R OMiCC Jamboree Working Group,: Dataset 3 in: Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity. F1000Research. 2016. Data Source
30. Lau WW Sparks R OMiCC Jamboree Working Group,: Dataset 4 in: Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity. F1000Research. 2016. Data Source