The bioinformatics core will provide analytical and statistical support for the various proposed projects. The core will also serve as a data repository for the high-throughput ChlP-seq data and will coordinate the deposition of the datasets into the public domain. Additionally, cytokine production and protein phosphorylation will be analyzed by core personnel with expertise in the BioPlex system. This POI project will study the molecular and cellular mechanisms of the induction and stability of regulatory T cells (Tregs). It involves the study of Tregs in both in vitro and in vivo models including molecular studies of gene transcriptional control and cellular studies using various mouse models of diseases. Particularly relevant to this core is the large amount of data that is expected as a result of the high-throughput techniques proposed. The core provide the following services: 1) to analyze and compare the data derived from ChlP-seq direct sequencing experiments performed for projects 1-4. 2) to perform statistical analyses of the experimental data from both in vitro and in vivo studies including those from various mouse models such as asthma, colitis, and viral infection. 3) to measure and analyze cytokine production and protein phosphorylation using the BioPlex system. The establishment of a core charged with these tasks will facilitate the consistent analysis of data sets as well as promote efficient and accurate data exchange among the various groups.

Public Health Relevance

Sophiscated data analysis is critical for the rational design and proper interpretaiton of the biological experiments. This bioinformatics core will be highly utilized by all projects, and will enable synergistic interactions among individual projects.

National Institute of Health (NIH)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
La Jolla Institute
La Jolla
United States
Zip Code
Baca Jones, Carmen; Pagni, Philippe P; Fousteri, Georgia et al. (2014) Regulatory T cells control diabetes without compromising acute anti-viral defense. Clin Immunol 153:298-307
Kong, Kok-Fai; Fu, Guo; Zhang, Yaoyang et al. (2014) Protein kinase C-? controls CTLA-4-mediated regulatory T cell function. Nat Immunol 15:465-72
Croft, Michael (2014) The TNF family in T cell differentiation and function--unanswered questions and future directions. Semin Immunol 26:183-90
Baca Jones, Carmen; Filippi, Christophe; Sachithanantham, Sowbarnika et al. (2014) Direct infection of dendritic cells during chronic viral infection suppresses antiviral T cell proliferation and induces IL-10 expression in CD4 T cells. PLoS One 9:e90855
Park, Yoon; Jin, Hyung-seung; Aki, Daisuke et al. (2014) The ubiquitin system in immune regulation. Adv Immunol 124:17-66
Madireddi, Shravan; Eun, So-Young; Lee, Seung-Woo et al. (2014) Galectin-9 controls the therapeutic activity of 4-1BB-targeting antibodies. J Exp Med 211:1433-48
Boettler, Tobias; Choi, Youn Soo; Salek-Ardakani, Shahram et al. (2013) Exogenous OX40 stimulation during lymphocytic choriomeningitis virus infection impairs follicular Th cell differentiation and diverts CD4 T cells into the effector lineage by upregulating Blimp-1. J Immunol 191:5026-35
Croft, Michael; Benedict, Chris A; Ware, Carl F (2013) Clinical targeting of the TNF and TNFR superfamilies. Nat Rev Drug Discov 12:147-68
Kim, Gisen; Shinnakasu, Ryo; Saris, Christiaan J M et al. (2013) A novel role for IL-27 in mediating the survival of activated mouse CD4 T lymphocytes. J Immunol 190:1510-8
Zhao, Yuan; Croft, Michael (2012) Dispensable role for 4-1BB and 4-1BBL in development of vaccinia virus-specific CD8 T cells. Immunol Lett 141:220-6

Showing the most recent 10 out of 12 publications