Implementation of exon arrays: Alternative splicing during T-cell proliferation as determined by whole genome analysis

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Whistler, Toni ^a   Chiang, Cheng Feng ^a   Lonergan, William ^a   Hollier, Mark ^a   Unger, Elizabeth R ^a  

^a NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ALTERNATIVE RNA SPLICING; ARTICLE; BIOGENESIS; CELL CYCLE; CELL DEATH; CELL DIVISION; CHROMOSOME SEGREGATION; CONTROLLED STUDY; EXON; FEMALE; FLOW CYTOMETRY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENETIC ORGANIZATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; HUMAN CELL; LYMPHOCYTE PROLIFERATION; METABOLISM; MICROARRAY ANALYSIS; PERIPHERAL BLOOD MONONUCLEAR CELL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPLICEOSOME; T LYMPHOCYTE; T LYMPHOCYTE ACTIVATION; APOPTOSIS; CELL PROLIFERATION; CLUSTER ANALYSIS; CYTOLOGY; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION PROFILING; GENETICS; HUMAN GENOME; IMMUNOLOGY; LYMPHOCYTE ACTIVATION; LYMPHOCYTE SUBPOPULATION; METHODOLOGY; MIDDLE AGED; POLYMERASE CHAIN REACTION; QUALITY CONTROL; REPRODUCIBILITY;

MESSENGER RNA; PHYTOHEMAGGLUTININ;

ALTERNATIVE SPLICING; APOPTOSIS; CELL CYCLE; CELL PROLIFERATION; CLUSTER ANALYSIS; EXONS; FEMALE; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; LYMPHOCYTE ACTIVATION; LYMPHOCYTE SUBSETS; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYTOHEMAGGLUTININS; POLYMERASE CHAIN REACTION; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; SPLICEOSOMES; T-LYMPHOCYTES;

EID: 77956492746     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-496     Document Type: Article

References (44)

1. Ramsborg CG, Papoutsakis ET. Global transcriptional analysis delineates the differential inflammatory response interleukin-15 elicits from cultured human T cells. Exp Hematol 2007, 35:454-464. 10.1016/j.exphem.2006.11.013, 1855244, 17309826.
2. Shaffer AL, Rosenwald A, Hurt EM, Giltnane JM, Lam LT, Pickeral OK, et al. Signatures of the immune response. Immunity 2001, 15:375-385. 10.1016/S1074-7613(01)00194-7, 11567628.
3. Ellisen LW, Palmer RE, Maki RG, Truong VB, Tamayo P, Oliner JD, et al. Cascades of transcriptional induction during human lymphocyte activation. Eur J Cell Biol 2001, 80:321-328. 10.1078/0171-9335-00162, 11432721.
4. Argyropoulos C, Nikiforidis GC, Theodoropoulou M, Adamopoulos P, Boubali S, Georgakopoulos TN, et al. Mining microarray data to identify transcription factors expressed in naive resting but not activated T lymphocytes. Genes Immun 2004, 5:16-25. 10.1038/sj.gene.6364034, 14735145.
5. Bunting K, Rao S, Hardy K, Woltring D, Denyer GS, Wang J, et al. Genome-wide analysis of gene expression in T cells to identify targets of the NF-kappa B transcription factor c-Rel. J Immunol 2007, 178:7097-7109.
6. Chtanova T, Newton R, Liu SM, Weininger L, Young TR, Silva DG, et al. Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets. J Immunol 2005, 175:7837-7847.
7. Hess K, Yang Y, Golech S, Sharov A, Becker KG, Weng NP. Kinetic assessment of general gene expression changes during human naive CD4+ T cell activation. Int Immunol 2004, 16:1711-1721. 10.1093/intimm/dxh172, 15492022.
8. Li XD, Essayan DM, Liu MC, Beaty TH, Huang SK. Profiling of differential gene expression in activated, allergen-specific human Th2 cells. Genes Immun 2001, 2:88-98. 10.1038/sj.gene.6363743, 11393662.
9. Li Y, Wong KK, Matsueda S, Efferson CL, Chang DZ, Ioannides CG, et al. Mitogen stimulation activates different signaling pathways in early- and late-divided T cells as revealed by cDNA microarray analysis. Int J Mol Med 2006, 18:1127-1139.
10. Lu B, Zagouras P, Fischer JE, Lu J, Li B, Flavell RA. Kinetic analysis of genomewide gene expression reveals molecule circuitries that control T cell activation and Th1/2 differentiation. Proc Natl Acad Sci USA 2004, 101:3023-3028. 10.1073/pnas.0307743100, 365738, 14978277.
11. Ip JY, Tong A, Pan Q, Topp JD, Blencowe BJ, Lynch KW. Global analysis of alternative splicing during T-cell activation. RNA 2007, 13:563-572. 10.1261/rna.457207, 1831861, 17307815.
12. Grigoryev YA, Kurian SM, Nakorchevskiy AA, Burke JP, Campbell D, Head SR, et al. Genome-wide analysis of immune activation in human T and B cells reveals distinct classes of alternatively spliced genes. PLoS One 2009, %19(4):e7906.
13. Affymetrix Exon probeset annotations and transcript cluster groupings. version 1. 2005, Affymetrix, Santa Clara, CA, Ref Type: Pamphlet, Affymetrix., http://www.affymetrix.com/support/technical/whitepapers/exon_probeset_trans_clust_whitepaper.pdf
14. Affymetrix GeneChip whole transcript (WT) sense target labeling assay manual. 2007, Santa Clara, CA, Affymetrix, Ref Type: Pamphlet, Affymetrix.
15. Affymetrix Exon array background correction. version 1.0. 2005, Affymetrix, Santa Clara, CA, Ref Type: Pamphlet, Affymetrix., http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf
16. Affymetrix QC Metrics for Exon and Gene Design Expression Arrays: A summary based on the Affymetrix Quality Assessment of Exon and Gene Arrays White Paper. 2008, Affymetrix, Santa Clara, CA, Ref Type: Pamphlet, Affymetrix.
17. Affymetrix Quality Assessment of Exon and Gene Arrays. 2007, Affymetrix, Santa Clara, CA, Ref Type: Pamphlet, Affymetrix.
18. Affymetrix Identifying and validating alternative splicing events: An introduction to managing data provided by GeneChip Exon arrays. 702422 Rev. 1. 2008, Santa Clara, CA, Affymetrix, Ref Type: Pamphlet, Affymetrix.
19. Affymetrix Alternative Transcript Analysis Methods for Exon Arrays. 2005, Affymetrix, Santa Clara, CA, Ref Type: Pamphlet, Affymetrix.
20. Palmer C, Diehn M, Alizadeh AA, Brown PO. Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics 2006, 7:115. 10.1186/1471-2164-7-115, 1479811, 16704732.
21. Lyons PA, Koukoulaki M, Hatton A, Doggett K, Woffendin HB, Chaudhry AN, et al. Microarray analysis of human leucocyte subsets: the advantages of positive selection and rapid purification. BMC Genomics 2007, 8:64. 10.1186/1471-2164-8-64, 1828063, 17338817.
22. Qu Y, He F, Chen Y. Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays. BMC Bioinformatics 2010, 11:211. 10.1186/1471-2105-11-211, 2873539, 20426803.
23. Storey J. The positive false discovery rate: A Bayesian interpretation and the q-value. Annals of Statistics 2003, 100:9445.
24. Whistler T, Chiang C, Lin JM, Lonergan W, Reeves W. The comparison of different pre- and post-analysis filters for determination of exon level alternative splicing events using Affymetrix arrays. Journal Biomolecular Techniques 2010, 21:44-53.
25. Della BC, Cordero F, Calogero RA. Dissecting an alternative splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays. BMC Genomics 2008, 9:571. 10.1186/1471-2164-9-571, 2612032, 19040723.
26. Gellert P, Uchida S, Braun T. Exon Array Analyzer: a web interface for Affymetrix exon array analysis. Bioinformatics 2009, 25:3323-3324. 10.1093/bioinformatics/btp577, 19808879.
27. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative CT method. Nat Protocols 2008, 3:1101-1108.
28. Yuan JS, Reed A, Chen F, Stewart CN. Statistical analysis of real-time PCR data. BMC Bioinformatics 2006, 7:85. 10.1186/1471-2105-7-85, 1395339, 16504059.
29. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2008, 36:D773-D779. 10.1093/nar/gkm966, 2238835, 18086701.
30. Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics 2008, 9:529. 10.1186/1471-2164-9-529, 2585104, 18990248.
31. Okoniewski MJ, Hey Y, Pepper SD, Miller CJ. High correspondence between Affymetrix exon and standard expression arrays. Biotechniques 2007, 42:181-185. 10.2144/000112315, 17373482.
32. Abdueva D, Wing MR, Schaub B, Triche TJ. Experimental comparison and evaluation of the Affymetrix exon and U133Plus2 GeneChip arrays. PLoS ONE 2007, 2:e913. 10.1371/journal.pone.0000913, 1976394, 17878948.
33. Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, et al. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 2006, 7:325. 10.1186/1471-2164-7-325, 1769375, 17192196.
34. Yeo GW, Xu X, Liang TY, Muotri AR, Carson CT, Coufal NG, et al. Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol 2007, 3:1951-1967. 10.1371/journal.pcbi.0030196, 2041973, 17967047.
35. Clark TA, Schweitzer AC, Chen TX, Staples MK, Lu G, Wang H, et al. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol 2007, 8:R64. 10.1186/gb-2007-8-4-r64, 1896007, 17456239.
36. Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet 2002, 30:13-19. 10.1038/ng0102-13, 11753382.
37. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003, 302:2141-2144. 10.1126/science.1090100, 14684825.
38. Lin Z, Fillmore GC, Um TH, Elenitoba-Johnson KS, Lim MS. Comparative microarray analysis of gene expression during activation of human peripheral blood T cells and leukemic Jurkat T cells. Lab Invest 2003, 83:765-776.
39. Asare AL, Kolchinsky SA, Gao Z, Wang R, Raddassi K, Bourcier K, et al. Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation. BMC Genomics 2008, 9:474. 10.1186/1471-2164-9-474, 2573897, 18847473.
40. Reddy M, Eirikis E, Davis C, Davis HM, Prabhakar U. Comparative analysis of lymphocyte activation marker expression and cytokine secretion profile in stimulated human peripheral blood mononuclear cell cultures: an in vitro model to monitor cellular immune function. J Immunol Methods 2004, 293:127-142. 10.1016/j.jim.2004.07.006, 15541283.
41. Pfoertner S, Jeron A, Probst-Kepper M, Guzman CA, Hansen W, Westendorf AM, et al. Signatures of human regulatory T cells: an encounter with old friends and new players. Genome Biol 2006, 7:R54. 10.1186/gb-2006-7-7-r54, 1779567, 16836768.
42. Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D, et al. Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci USA 2002, 99:11796-11801. 10.1073/pnas.092284399, 129348, 12195013.
43. Chen L. A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms. Nucleic Acids Res 2010, 38:1086-1097. 10.1093/nar/gkp1136, 2831334, 19969546.
44. Long JC, Caceres JF. The SR protein family of splicing factors: master regulators of gene expression. Biochem J 2009, 417:15-27. 10.1042/BJ20081501, 19061484.