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 higherorder 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 loglinear 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 co...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Mark C. Emerick, Giovanni Parmigiani, William S. Agnew
• Keywords: BMCBI 2007, Correlations, Pair-wise Correlation, Single Gene