Multivariate analysis and visualization of splicing correlations in single-gene transcriptomes.
BACKGROUND
RNA metabolism, through 'combinatorial splicing', can generate enormous structural diversity in the proteome. Alternative domains may interact, however, with unpredictable phenotypic consequences, necessitating integrated RNA-level regulation of molecular composition. Splicing correlations within transcripts of single genes provide valuable clues to functional relationships among molecular domains as well as genomic targets for higher-order splicing regulation.


RESULTS
We present tools to visualize complex splicing patterns in full-length cDNA libraries. Developmental changes in pair-wise correlations are presented vectorially in 'clock plots' and linkage grids. Higher-order correlations are assessed statistically through Monte Carlo analysis of a log-linear model with an empirical-Bayes estimate of the true probabilities of observed and unobserved splice forms. Log-linear coefficients are visualized in a 'spliceprint,' a signature of splice correlations in the transcriptome. We present two novel metrics: the linkage change index, which measures the directional change in pair-wise correlation with tissue differentiation, and the accuracy index, a very simple goodness-of-fit metric that is more sensitive than the integrated squared error when applied to sparsely populated tables, and unlike chi-square, does not diverge at low variance. Considerable attention is given to sparse contingency tables, which are inherent to single-gene libraries.


CONCLUSIONS
Patterns of splicing correlations are revealed, which span a broad range of interaction order and change in development. The methods have a broad scope of applicability, beyond the single gene--including, for example, multiple gene interactions in the complete transcriptome.
Emerick
Mark C
MC
Department of Physiology, Johns Hopkins Medical School, Baltimore, MD 21205 USA. memeri@jhmi.edu
Parmigiani
Giovanni
G
Agnew
William S
WS
D017398:Alternative Splicing / Q000235:genetics; D015723:Gene Library; D014644:Genetic Variation / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D015999:Multivariate Analysis; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics*; D017381:Spliceosomes / Q000737:chemistry / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*
D022821:RNA Splice Sites