Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts

As a fruit of the current revolution in sequencing technology, transcriptomes can now be analyzed at an unprecedented level of detail. These advances have been exploited for detecting differential expressed genes across biological samples and for quantifying the abundances of various RNA transcripts within one gene. However, explicit strategies for detecting the hidden differential abundances of RNA transcripts in biological samples have not been defined. In this work, we present two novel statistical tests to address this issue: a 'gene structure sensitive' Poisson test for detecting differential expression when the transcript structure of the gene is known, and a kernel-based test called Maximum Mean Discrepancy when it is unknown. We analyzed the proposed approaches on simulated read data for two artificial samples as well as on factual reads generated by the Illumina Genome Analyzer for two _C. elegans_ samples. Our analysis shows that the Poisson test identifies genes with differential transcript expression considerably better that previously proposed RNA transcript quantification approaches for this task. The MMD test is able to detect a large fraction (75%) of such differential cases without the knowledge of the annotated transcripts. It is therefore well-suited to analyze RNA-Seq experiments when the genome annotations are incomplete or not available, where other approaches have to fail

EXTEND-L : an input language for extensible register transfer compilation

This report discusses the model and input language for EXTEND, a synthesis system that permits extensible register transfer synthesis. EXTEND-L fills the need for a language that bridges the gap between existing behavioral input descriptions, which are too abstract, and structural schematics, which cannot capture the high-level behavior. The report first discusses previous work in behavioral synthesis and summarizes the deficiencies of these behavioral specifications. The report then describes the proposed langauge in detail, and concludes with a few examples that show its utility

Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq

Additional file 6. Half site analysis for BATFx-JUNB-IRFx. (A) Single variants from half sites of these oligos in the library were used to generate energy logos. Bolded positions represent the half sites generated in B. (B) Energy logos from Spec-seq results of BATFx-JUNB-IRFx. The Y-axis is negative energy so the preferred sequence is on the top