Transcriptomic Data Analysis Using Graph-Based Out-of-Core Methods

Biological data derived from high-throughput microarrays can be transformed into finite, simple, undirected graphs and analyzed using tools first introduced by the Langston Lab at the University of Tennessee. Transforming raw data can be broken down into three main tasks: data normalization, generation of similarity metrics, and threshold selection. The choice of methods used in each of these steps effect the final outcome of the graph, with respect to size, density, and structure. A number of different algorithms are examined and analyzed to illustrate the magnitude of the effects. Graph-based tools are then used to extract putative gene networks. These tools are loosely based on the concept of clique, which generates clusters optimized for density. Innovative additions to the paraclique algorithm, developed at the Langston Lab, are introduced to generate results that have highest average correlation or highest density. A new suite of algorithms is then presented that exploits the use of a priori gene interactions. Aptly named the anchored analysis toolkit, these algorithms use known interactions as anchor points for generating subgraphs, which are then analyzed for their graph structure. This results in clusters that might have otherwise been lost in noise. A main product of this thesis is a novel collection of algorithms to generate exact solutions to the maximum clique problem for graphs that are too large to fit within core memory. No other algorithms are currently known that produce exact solutions to this problem for extremely large graphs. A combination of in-core and out-of-core techniques is used in conjunction with a distributed-memory programming model. These algorithms take into consideration such pitfalls as external disk I/O and hardware failure and recovery. Finally, a web-based tool is described that provides researchers access the aforementioned algorithms. The Graph Algorithms Pipeline for Pathway Analysis tool, GrAPPA, was previously developed by the Langston Lab and provides the software needed to take raw microarray data as input and preprocess, analyze, and post-process it in a single package. GrAPPA also provides access to high-performance computing resources, via the TeraGrid

Geraldton region land resources survey

This report presents results from soil and landform mapping at a scale of 1:250,000 for approximately 2.1 million hectares of the wheat-sheep belt of Western Australia. The study area corresponds with the Geraldton advisory district for Agriculture Western Australia and is the northern extent of the wheatbelt. The area covers parts of three major geological regions of Western Australia: the Perth Basin, Carnarvon Basin and the Yilgarn Craton. Fifty-one soil-landscape systems have been identified, some of which have been divided into subsystems, and are illustrated on the accompanying maps. The landform, parent material, rainfall, land use, native vegetation and soils are described within the text. Forty-eight soil series are described. Five soil properties and six degradation risks are described for each soil series. The areas for each system are indicated with approximate proportions for soils. The report provides an inventory of the soil and land resources of the Geraldton agricultural region for use in regional land use planning and interpretation

Graph algorithms for machine learning: a case-control study based on prostate cancer populations and high throughput transcriptomic data

Background The continuing proliferation of high-throughput biological data promises to revolutionize personalized medicine. Confirming the presence or absence of disease is an important goal. In this study, we seek to identify genes, gene products and biological pathways that are crucial to human health, with prostate cancer chosen as the target disease. Materials and methods Using case-control transcriptomic data, we devise a graph theoretical toolkit for this task. It employs both innovative algorithms and novel two-way correlations to pinpoint putative biomarkers that classify unknown samples as cancerous or normal. Results and conclusion Observed accuracy on real data suggests that we are able to achieve sensitivity of 92% and specificity of 91%

Natural resources of Lake Earl and Smith River Delta

The Lake Earl/Smith River Delta area is a key coastal wetland situated in northern California. The Lake and Delta have retained much of their value to wildlife and serve as an important link in a chain of such wetlands that extend southward along the Pacific Ocean from Alaska to South America. Millions of water-associated birds of the Pacific Flyway utilize these areas as feeding and resting stops along their migration paths. In California, these wetlands also serve as a significant portion of the available wintering grounds for a major share of the birds within the flyway. The Smith River is also one of the State's most productive salmon and steelhead streams. Anadromous fish produced here provide thousands of angler use days to sport fishermen and contribute substantially to the commercial fishing catch off the northern coast. Because of the importance of coastal wetlands to the fish and wildlife of California, the Department of Fish and Game has initiated a high priority statewide inventory and assessment of these wetlands. This publication is an integral part of that program. This report identifies specific resources and uses; directs attention to problems; and recommends courses of action needed to insure resource protection. It is intended as a guide for citizens, planners, administrators and other interested in the use and development of California's coastal land and waters. (132pp.

MIL evaluation of center pivot irrigation systems

Presented at the 2006 Central Plains irrigation conference on February 21-22 in Colby, Kansas.Includes bibliographical references

Irrigation and drainage in the new millennium

Presented at the 2000 USCID international conference, Challenges facing irrigation and drainage in the new millennium on June 20-24 in Fort Collins, Colorado.Irrigation scheduling has been promoted as management tool to minimize irrigation water application, however, few irrigators regularly followed any rigorous scheduling methodology. Kansas State University Research and Extension in conjunction with an irrigation association, Water PACK, began a long-term project to promote ET based irrigation scheduling and other management technology. Area irrigators serve as the focal point of the project and over time have been asked to assume responsibility of scheduling the project fields. A long-term commitment and on-farm activities such as variable water application tests and center pivot uniformity tests seems to have generated confidence and acceptance of ET-based irrigation scheduling

Inferring gene coexpression networks for low dose ionizing radiation using graph theoretical algorithms and systems genetics

Background Biological data generated through large scale -omics technologies have resulted in a new paradigm in the study of biological systems. Instead of focusing on individual genes or proteins these technologies enable us to extract biological networks using powerful computing and statistical algorithms that are scalable to very large datasets. Materials and methods We have developed a tool chain using novel graph algorithms to extract gene coexpression networks from microarray data. We highlight implementation of our tool chain to investigate the effects of in vivo low dose ionizing radiation treatments on mice. We are using systems genetics approach to investigate the biological effects of low dose (10 cGy) ionizing radiation. We measured the base line gene expression profile from spleen tissue of BXD recombinant inbred mice using Illumina microarrays. The data was filtered using coefficient of variance after robust spline normalization and variance stabilizing transformation. A graph was then derived from this data, with probes as vertices and edges between them representing correlations. The graph was analyzed using our toolkit to find the size and number of maximal cliques. We deployed another tool called paraclique that relaxes clique’s requirement that every edge be present between all vertices. Paraclique enables us to account for inherent noise in the microarray data and stochastic nature of biological processes. Using immunophenotype data from the baseline BXD mice, we employed biclique analysis to determine interactions between genotypes and immunophenotypes (%CD4, %CD3, LN T:B, %CD8, and LN CD4:CD8). We also extracted eQTLs from BXD data using QTL-Reaper from base line gene expression profiles. 1881 transcripts were associated with 686 loci. The eQTLs were classified as cis or trans according to their genomic positions. Besides population level studies we also investigated the differential effect of low dose and high dose (1Gy) of ionizing radiations on spleen gene expression in inbred parental strains (C57BL/6J and DBA/2J) of BXD recombinant inbred mice as well as BALB/c mice, a known radiation-sensitive strain

Stable isotopes infer the diet and habitat of the enigmatic pygmy right whale (Caperea marginata) off southern Australia

In the Southern Hemisphere, baleen whales generally undertake migrations between productive feeding grounds at high latitudes and breeding grounds at lower latitudes. Pygmy right whales (Caperea marginata) (PRW) are the smallest and most enigmatic baleen whale, that likely forgo long-distance migrations, and instead inhabit temperate and subantarctic waters year-round. Previous research has relied on limited data from sighting and stranding records to infer the habitat use and diet of PRWs, however the absence of long-term and consistent data has left uncertainty surrounding these parameters. We utilized bulk stable isotopes of carbon (δ13C) and nitrogen (δ15N) in baleen from Australian PRWs (n = 14) to infer their diet and habitat use. Stable isotope values from 1980–2019 were then matched to remote sensed data from known upwelling regions (where they likely feed) to examine if their dietary patterns are related to changes in food web dynamics. We found that PRWs remained in mid-latitude waters year-round and showed no evidence of feeding in Antarctic waters. Rather, their isotopic record suggests they remain between coastal waters off southern Australia and the Subtropical Convergence, feeding on krill and copepods. Additionally, there was a weak positive relationship between PRW nitrogen stable isotope values and sea surface temperature (SST) from the eastern Great Australian Bight (GAB) and Bonney Upwelling. This suggests seasonal changes in their diet is possibly correlated to oceanographic changes which drive food-web dynamics in these regions. Unlike larger species of baleen whales that migrate further to highly productive waters in the Southern Ocean to meet their energetic demands, the small PRW, who only reach 6.5m, may sustain both feeding and breeding requirements at mid-latitudes. This is the first study to analyze long-term dietary and movement patterns of the PRW, providing an important contribution to our understanding of the species