Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries.

Background: The joint analysis of several categorical variables is a common task in many areas of biology, and is becoming central to systems biology investigations whose goal is to identify potentially complex interaction among variables belonging to a network. Interactions of arbitrary complexity are traditionally modeled in statistics by log-linear models. It is challenging to extend these to the high dimensional and potentially sparse data arising in computational biology.

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.

Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations.

We describe the regulated transcriptome of CACNA1G, a human gene for T-type Ca(v)3.1 calcium channels that is subject to extensive alternative RNA splicing. Fifteen sites of transcript variation include 2 alternative 5'-UTR promoter sites, 2 alternative 3'-UTR polyadenylation sites, and 11 sites of alternative splicing within the open reading frame.

The effect of higher order RNA processes on changing patterns of protein domain selection: a developmentally regulated transcriptome of type 1 inositol 1,4,5-trisphosphate receptors.

The domain structure of proteins synthesized from a single gene can be remodeled during tissue development by activities at the RNA level of gene expression. The impact of higher order RNA processing on changing patterns of protein domain selection may be explored by systematically profiling single-gene transcriptomes. itpr1 is one of three mammalian genes encoding receptors for the second messenger inositol 1,4,5-trisphosphate (InsP3).