POPLAR GENE EXPRESSION DATA ANALYSIS PIPELINES

Analyzing large-scale gene expression data is a labor-intensive and time-consuming process. To make data analysis easier, we developed a set of pipelines for rapid processing and analysis poplar gene expression data for knowledge discovery. Of all pipelines developed, differentially expressed genes (DEGs) pipeline is the one designed to identify biologically important genes that are differentially expressed in one of multiple time points for conditions. Pathway analysis pipeline was designed to identify the differentially expression metabolic pathways. Protein domain enrichment pipeline can identify the enriched protein domains present in the DEGs. Finally, Gene Ontology (GO) enrichment analysis pipeline was developed to identify the enriched GO terms in the DEGs. Our pipeline tools can analyze both microarray gene data and high-throughput gene data. These two types of data are obtained by two different technologies. A microarray technology is to measure gene expression levels via microarray chips, a collection of microscopic DNA spots attached to a solid (glass) surface, whereas high throughput sequencing, also called as the next-generation sequencing, is a new technology to measure gene expression levels by directly sequencing mRNAs, and obtaining each mRNA’s copy numbers in cells or tissues. We also developed a web portal (http://sys.bio.mtu.edu/) to make all pipelines available to public to facilitate users to analyze their gene expression data. In addition to the analyses mentioned above, it can also perform GO hierarchy analysis, i.e. construct GO trees using a list of GO terms as an input.

Seismic Serviceability Assessment of Water Distribution Systems

Water distribution systems are important for life saving facilities especially in the recovery after earthquakes. In this paper, a framework is discussed about seismic serviceability of water systems that includes the fragility evaluation of water sources of water distribution networks. Also, a case study is brought about the performance of a water system under different levels of seismic hazard. The seismic serviceability of a water supply system provided by EPANET is evaluated under various levels of seismic hazard. Basically, the assessment process is based on hydraulic analysis and Monte Carlo simulations, implemented with empirical fragility data provided by the American Lifeline Alliance (ALA, 2001) for both pipelines and water facilities. Represented by the Seismic Serviceability Index (Cornell University, 2008), the serviceability of the water distribution system is evaluated under each level of earthquakes with return periods of 72 years, 475 years, and 2475 years. The system serviceability under levels of earthquake hazard are compared with and without considering the seismic fragility of the water source. The results show that the seismic serviceability of the water system decreases with the growing of the return period of seismic hazard, and after considering the seismic fragility of the water source, the seismic serviceability decreases. The results reveal the importance of considering the seismic fragility of water sources, and the growing dependence of the system performance of water system on the seismic resilience of water source under severe earthquakes.