NDLI: Genetic modulation during thymocyte development an integrative approach based on microarray meta-analysis

Content Provider	IEEE Xplore Digital Library
Author	Palu, C.C. Linhares-Lacerda, L. Savino, W. Ribeiro-Alves, M.
Copyright Year	2015
Description	Author affiliation: Lab. on Thymus Res., Oswaldo Cruz Found., Rio de Janeiro, Brazil (Palu, C.C.; Linhares-Lacerda, L.; Savino, W.) \|\| Clinical Res. Lab. in Sexually-Transmitted Diseases-AIDS, Oswaldo Cruz Found., Rio de Janeiro, Brazil (Ribeiro-Alves, M.)
Abstract	The thymus is a primary lymphoid organ where T cell development takes place. The alpha-beta T lymphocyte lineage has well defined developmental stages, wherein the T cell receptor (TCR) structure and interaction ability are tested so that to guarantee central tolerance in the immune system. We conducted a meta-analysis using microarray data of T cell precursors (thymocytes) but only experiments where the thymocytes were isolated based on the developmental stages defined by the expression of CD4 and CD8 markers. Our approach allowed us to isolate meaningfully different gene categories regardless of the microarray platform, and to provide a perspective on gene modulation during this process. After filtering the data, the remaining 991 genes were sorted according to their expression profile across 27 comparisons, resulting in 15 clusters. We coupled the cluster expression profiles with the evidence in the literature, providing a comprehensive view of thymocyte development. As expected, our results associate the gene expression with TCR signaling pathways. Additionally, they revealed new genes associated with this process, and provided more evidence to understand the role of genes already known to be important to T cell development. Lastly, the clusters were related with other surface receptor signaling pathways, as well as chemotaxis and cell migration process, highlighting the importance of external stimuli to thymocyte differentiation. In conclusion, we have identified, through data integration, pathways and molecules that should have relevant impact on T cell development. We believe that the meta-analysis reported herein improved the comprehension on how the gene expression is organized temporally, providing a global perspective on the thymocyte gene modulation waves.
Starting Page	1
Ending Page	6
File Size	492971
Page Count	6
File Format	PDF
e-ISBN	9781467396639
DOI	10.1109/ICCABS.2015.7344708
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-10-15
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Context Integrative analysis T cell development Thymocyte Microarray metaanalysis Modulation Clustering algorithms Software Mice Gene expression Probes
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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