Beyond the transcriptome: completion of act one of the Immunological Genome Project

Current Opinion in Immunology

Volumn 25, Issue 5, 2013, Pages 593-597

  Kim, Charles C ^a   Lanier, Lewis L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTERLEUKIN 7; TRANSCRIPTOME; VASCULOTROPIN A;

CD8+ T LYMPHOCYTE; GENE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC VARIATION; GENOME; GENOME ANALYSIS; HUMAN; IL7 GENE; IMMUNOLOGICAL GENOME; NATURAL KILLER CELL; NONHUMAN; PHENOTYPE; REVIEW; RNA SEQUENCE; SEQUENCE ANALYSIS; T LYMPHOCYTE ACTIVATION; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; VEGFA GENE; ANIMAL; GENETIC TRANSCRIPTION; IMMUNE SYSTEM; IMMUNOLOGY; LEUKOCYTE;

ANIMALS; GENE REGULATORY NETWORKS; GENOME; HUMANS; IMMUNE SYSTEM; LEUKOCYTES; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84898018103     PISSN: 09527915     EISSN: 18790372     Source Type: Journal    
DOI: 10.1016/j.coi.2013.09.013     Document Type: Review

References (24)

1. 1•• Benoist, C., Germain, R.N., Mathis, D., A plaidoyer for systems immunology. Immunol Rev 210 (2006), 229–234 An eloquent perspective on the value of systems immunology and the challenges it faces in a historically hypothesis-focused system.
2. 2 Germain, R.N., Meier-Schellersheim, M., Nita-Lazar, A., Fraser, I.D.C., Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol 29 (2011), 527–585.
3. 3 Woese, C.R., Fox, G.E., Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74 (1977), 5088–5090.
4. 4 Dagan, T., Phylogenomic networks. Trends Microbiol 19 (2011), 483–491.
5. 5 Benoist, C., Lanier, L., Merad, M., Mathis, D., Consortium biology in immunology: the perspective from the Immunological Genome Project. Nat Rev Immunol 12 (2012), 734–740.
6. 6 Hyatt, G., Melamed, R., Park, R., Seguritan, R., Laplace, C., Poirot, L., Zucchelli, S., Obst, R., Matos, M., Venanzi, E., et al. Gene expression microarrays: glimpses of the immunological genome. Nat Immunol 7 (2006), 686–691.
7. 7 Shay, T., Kang, J., Immunological Genome Project and systems immunology. Trends Immunol, 2013 pii:S1471-4906(13)00049-5.
8. 8 Heng, T.S.P., Painter, M.W., The Immunological Genome Project: networks of gene expression in immune cells. Nat Immunol 9 (2008), 1091–1094.
9. 9 Chow, A., Brown, B.D., Merad, M., Studying the mononuclear phagocyte system in the molecular age. Nat Rev Immunol 11 (2011), 788–798.
10. 10 Mabbott, N.A., Kenneth Baillie, J., Hume, D.A., Freeman, T.C., Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations. Immunobiology 215 (2010), 724–736.
11. 11 Hume, D.A., Summers, K.M., Raza, S., Baillie, J.K., Freeman, T.C., Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations. Genomics 95 (2010), 328–338.
12. 12• Gautier, E.L., Shay, T., Miller, J., Greter, M., Jakubzick, C., Ivanov, S., Helft, J., Chow, A., Elpek, K.G., Gordonov, S., et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol 13 (2012), 1118–1128 Proposes the use of MerTK and CD64 to distinguish macrophages from dendritic cells.
13. 13• Miller, J.C., Brown, B.D., Shay, T., Gautier, E.L., Jojic, V., Cohain, A., Pandey, G., Leboeuf, M., Elpek, K.G., Helft, J., et al. Deciphering the transcriptional network of the dendritic cell lineage. Nat Immunol 13 (2012), 888–899 Investigates a large number of dendritic cell subsets at the molecular level, including identification of candidate regulators of dendritic cell diversity.
14. 14 Narayan, K., Sylvia, K.E., Malhotra, N., Yin, C.C., Martens, G., Vallerskog, T., Kornfeld, H., Xiong, N., Cohen, N.R., Brenner, M.B., et al. Intrathymic programming of effector fates in three molecularly distinct γδT cell subtypes. Nat Immunol 13 (2012), 511–518.
15. 15 Bezman, N.A., Kim, C.C., Sun, J.C., Min-Oo, G., Hendricks, D.W., Kamimura, Y., Best, J.A., Goldrath, A.W., Lanier, L.L., Molecular definition of the identity and activation of natural killer cells. Nat Immunol 13 (2012), 1000–1009.
16. 16 Sun, J.C., Beilke, J.N., Lanier, L.L., Adaptive immune features of natural killer cells. Nature 457 (2009), 557–561.
17. 17• Cohen, N.R., Brennan, P.J., Shay, T., Watts, G.F., Brigl, M., Kang, J., Brenner, M.B., Monach, P., Shinton, S.A., Hardy, R.R., et al. Shared and distinct transcriptional programs underlie the hybrid nature of iNKT cells. Nat Immunol 14 (2013), 90–99 Addresses questions about subset diversity in iNKT cells and the relatedness of these subsets to one another and other lymphocyte populations.
18. 18 Malhotra, D., Fletcher, A.L., Astarita, J., Lukacs-Kornek, V., Tayalia, P., Gonzalez, S.F., Elpek, K.G., Chang, S.K., Knoblich, K., Hemler, M.E., et al. Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks. Nat Immunol 13 (2012), 499–510.
19. 19 Best, J.A., Blair, D.A., Knell, J., Yang, E., Mayya, V., Doedens, A., Dustin, M.L., Goldrath, A.W., Monach, P., Shinton, S.A., et al. Transcriptional insights into the CD8(+) T cell response to infection and memory T cell formation. Nat Immunol 14:4 (2013), 404–412.
20. 20 Germain, R.N., Maintaining system homeostasis: the third law of Newtonian immunology. Nat Immunol 13 (2012), 902–906.
21. 21 Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D., Friedman, N., Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34 (2003), 166–176.
22. 22 Basso, K., Margolin, A.A., Stolovitzky, G., Klein, U., Dalla-Favera, R., Califano, A., Reverse engineering of regulatory networks in human B cells. Nat Genet 37 (2005), 382–390.
23. 23 Doering, T.A., Crawford, A., Angelosanto, J.M., Paley, M.A., Ziegler, C.G., Wherry, E.J., Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. Immunity 37 (2012), 1130–1144.
24. 24 Wang, Z., Gerstein, M., Snyder, M., RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10 (2009), 57–63.