Gene set bagging for estimating replicability of gene set analyses

Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach, called gene set bagging, for measuring the stability of ranking procedures using predefined gene sets. Gene set bagging involves resampling the original high-throughput data, performing gene-set analysis on the resampled data, and confirming that biological categories replicate. This procedure can be thought of as bootstrapping gene-set analysis and can be used to determine which are the most reproducible gene sets. Results: Here we apply this approach to two common genomics applications: gene expression and DNA methylation. Even with state-of-the-art statistical ranking procedures, significant categories in a gene set enrichment analysis may be unstable when subjected to resampling. Conclusions: We demonstrate that gene lists are not necessarily stable, and therefore additional steps like gene set bagging can improve biological inference of gene set analysis.Comment: 3 Figure

Looking for Pure Rotational H_2 Emission from Protoplanetary Disks

We report on a limited search for pure-rotational molecular hydrogen emission associated with young, pre-main-sequence stars. We looked for H_2 v=0 J = 3->1 and J = 4->2 emission in the mid-infrared using the Texas Echelon-Cross-Echelle Spectrograph (TEXES) at NASA's 3m Infrared Telescope Facility. The high spectral and spatial resolution of our observations lead to more stringent limits on narrow line emission close to the source than previously achieved. One star, AB Aur, shows a possible (2sigma) H_2 detection, but further observations are required to make a confident statement. Our non-detections suggest that a significant fraction, perhaps all, of previously reported H_2 emission towards these objects could be extended on scales of 5" or more.Comment: 14 pages including 2 figures. Accepted by ApJ Letter

Electric-field-induced phase transformation at a lead-free morphotropic phase boundary: Case study in a 93%(Bi0.5Na0.5)TiO3-7% BaTiO3 piezoelectric ceramic

The electric-field-induced strain in 93%(Bi0.5Na0.5)TiO3-7%BaTiO3 polycrystalline ceramic is shown to be the result of an electric-field-induced phase transformation from a pseudocubic to tetragonal symmetry. High-energy x-ray diffraction is used to illustrate the microstructural nature of the transformation. A combination of induced unit cell volumetric changes, domain texture, and anisotropic lattice strains are responsible for the observed macroscopic strain. This strain mechanism is not analogous to the high electric-field-induced strains observed in lead-based morphotropic phase boundary systems. Thus, systems which appear cubic under zero field should not be excluded from the search for lead-free piezoelectric compositions.open1127