The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp).

Molecular cloning and characterization of a novel gene upregulated early during postnatal rat lung development.

Alveoli form, in part, by subdivision (septation) of saccules constituting the gas exchange region of the immature lung. Rat lungs septate from postnatal day 4 through 14 but alveoli in male rats continue to form, by other means, until about age 44 days. In rats, we sought to identify genes involved in septation. Using differential display reverse transcription polymerase chain reaction, we cloned a cDNA, rA5D3, that had 1270 bp with an open reading frame encoding a putative polypeptide of 165 amino acids containing potential leucine zipper motifs and phosphorylation sites. Database searches indicated rA5D3 was a novel gene. rA5D3 RNA relative concentration increased 1.7-fold between postnatal days 4 and 8, decreased 4-fold between days 8 and 14, declined significantly thereafter but was still detected post alveolus formation. If the expression of rA5D3 protein resembles its RNA, its peak (postnatal day 8) is well after the onset of septation, suggesting a role other than the initiation of septation.