Differential Splicing Using Whole-transcript Microarrays

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2009 May 26

PMID 19463149

Citations 12

Authors

Mark D Robinson

Terence P Speed

Affiliations

Soon will be listed here.

Abstract

Background: The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0 ST (sense target) platform, with versions for Human, Mouse and Rat, is designed primarily to probe every known or predicted exon. The smaller Gene 1.0 ST array is designed as an expression microarray but still interrogates expression with probes along the full length of each well-characterized transcript. We explore the possibility of using the Gene 1.0 ST platform to identify differential splicing events.

Results: We propose a strategy to score differential splicing by using the auxiliary information from fitting the statistical model, RMA (robust multichip analysis). RMA partitions the probe-level data into probe effects and expression levels, operating robustly so that if a small number of probes behave differently than the rest, they are downweighted in the fitting step. We argue that adjacent poorly fitting probes for a given sample can be evidence of differential splicing and have designed a statistic to search for this behaviour. Using a public tissue panel dataset, we show many examples of tissue-specific alternative splicing. Furthermore, we show that evidence for putative alternative splicing has a strong correspondence between the Gene 1.0 ST and Exon 1.0 ST platforms.

Conclusion: We propose a new approach, FIRMAGene, to search for differentially spliced genes using the Gene 1.0 ST platform. Such an analysis complements the search for differential expression. We validate the method by illustrating several known examples and we note some of the challenges in interpreting the probe-level data.Software implementing our methods is freely available as an R package.

Citing Articles

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Stokes T, Cen H, Kapranov P, Gallagher I, Pitsillides A, Volmar C Adv Genet (Hoboken). 2023; 4(2):2200024.

PMID: 37288167 PMC: 10242409. DOI: 10.1002/ggn2.202200024.

Comprehensive analysis of prognostic genes in gastric cancer.

Huang S, Ma L, Lan B, Liu N, Nong W, Huang Z Aging (Albany NY). 2021; 13(20):23637-23651.

PMID: 34686626 PMC: 8580339. DOI: 10.18632/aging.203638.

A Computational Analysis of Alternative Splicing across Mammalian Tissues Reveals Circadian and Ultradian Rhythms in Splicing Events.

El-Athman R, Knezevic D, Fuhr L, Relogio A Int J Mol Sci. 2019; 20(16).

PMID: 31443305 PMC: 6721216. DOI: 10.3390/ijms20163977.

iGEMS: an integrated model for identification of alternative exon usage events.

Sood S, Szkop K, Nakhuda A, Gallagher I, Murie C, Brogan R Nucleic Acids Res. 2016; 44(11):e109.

PMID: 27095197 PMC: 4914109. DOI: 10.1093/nar/gkw263.

TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.

Chitturi N, Balagannavar G, Chandrashekar D, Abinaya S, S Srini V, K Acharya K BMC Genomics. 2013; 14:922.

PMID: 24373374 PMC: 3884118. DOI: 10.1186/1471-2164-14-922.

References

Grabowski P, Black D . Alternative RNA splicing in the nervous system. Prog Neurobiol. 2001; 65(3):289-308. DOI: 10.1016/s0301-0082(01)00007-7. View

Pan Q, Shai O, Lee L, Frey B, Blencowe B . Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008; 40(12):1413-5. DOI: 10.1038/ng.259. View

Xu Q, Modrek B, Lee C . Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res. 2002; 30(17):3754-66. PMC: 137414. DOI: 10.1093/nar/gkf492. View

Duan S, Zhang W, Bleibel W, Cox N, Dolan M . SNPinProbe_1.0: a database for filtering out probes in the Affymetrix GeneChip human exon 1.0 ST array potentially affected by SNPs. Bioinformation. 2008; 2(10):469-70. PMC: 2561168. DOI: 10.6026/97320630002469. View

Irizarry R, Bolstad B, Collin F, Cope L, Hobbs B, Speed T . Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):e15. PMC: 150247. DOI: 10.1093/nar/gng015. View

Robinson M, Speed T . A comparison of Affymetrix gene expression arrays. BMC Bioinformatics. 2007; 8:449. PMC: 2216046. DOI: 10.1186/1471-2105-8-449. View

Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S . Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMC: 545600. DOI: 10.1186/gb-2004-5-10-r80. View

Yeo G, Holste D, Kreiman G, Burge C . Variation in alternative splicing across human tissues. Genome Biol. 2004; 5(10):R74. PMC: 545594. DOI: 10.1186/gb-2004-5-10-r74. View

Schwerk C, Schulze-Osthoff K . Regulation of apoptosis by alternative pre-mRNA splicing. Mol Cell. 2005; 19(1):1-13. DOI: 10.1016/j.molcel.2005.05.026. View

10.

Gupta S, Zink D, Korn B, Vingron M, Haas S . Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing. BMC Genomics. 2004; 5:72. PMC: 521684. DOI: 10.1186/1471-2164-5-72. View

11.

Singh N, Preiser P, Renia L, Balu B, Barnwell J, Blair P . Conservation and developmental control of alternative splicing in maebl among malaria parasites. J Mol Biol. 2004; 343(3):589-99. DOI: 10.1016/j.jmb.2004.08.047. View

12.

Purdom E, Simpson K, Robinson M, Conboy J, Lapuk A, Speed T . FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics. 2008; 24(15):1707-14. PMC: 2638867. DOI: 10.1093/bioinformatics/btn284. View

13.

Huang J, Morris Q, Hughes T, Frey B . GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. Bioinformatics. 2005; 21 Suppl 1:i222-31. DOI: 10.1093/bioinformatics/bti1045. View

14.

French P, Peeters J, Horsman S, Duijm E, Siccama I, van den Bent M . Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. Cancer Res. 2007; 67(12):5635-42. DOI: 10.1158/0008-5472.CAN-06-2869. View

15.

Venables J . Aberrant and alternative splicing in cancer. Cancer Res. 2004; 64(21):7647-54. DOI: 10.1158/0008-5472.CAN-04-1910. View

16.

Wang E, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C . Alternative isoform regulation in human tissue transcriptomes. Nature. 2008; 456(7221):470-6. PMC: 2593745. DOI: 10.1038/nature07509. View

17.

Zhang W, Duan S, Bleibel W, Wisel S, Huang R, Wu X . Identification of common genetic variants that account for transcript isoform variation between human populations. Hum Genet. 2008; 125(1):81-93. PMC: 2665168. DOI: 10.1007/s00439-008-0601-x. View

18.

Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View

19.

Johnson J, Castle J, Garrett-Engele P, Kan Z, Loerch P, Armour C . Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science. 2003; 302(5653):2141-4. DOI: 10.1126/science.1090100. View

20.

Gardina P, Clark T, Shimada B, Staples M, Yang Q, Veitch J . Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006; 7:325. PMC: 1769375. DOI: 10.1186/1471-2164-7-325. View