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A Tissue Specific Transcriptomic, Proteomic And Phospho-Proteomic Atlas Of The Translational Machinery Of Arabidopsis Thaliana, Abdullah Salim

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Gene expression encompasses the flow of genetic information from DNA to mRNA (transcription) and from mRNA to protein (translation) along with the regulatory mechanisms underlying these processes. Omics technologies offer a powerful toolset with which to study gene expression at each of these stages. A recently published dataset integrating transcriptomic, proteomic and phospho-proteomic measurements from 30 Arabidopsis thaliana tissues provides a unique resource to explore gene expression.¹ The translational machinery (the ribosome, and its initiation, elongation, and termination factors) are a core component in gene expression. Defects in translation can be lethal or lead to major developmental defects and …

High Variance In Reproductive Success Generates A False Signature Of A Genetic Bottleneck In Populations Of Constant Size: A Simulation Study, Sean M. Hoban, Massimo Mezzavilla, Oscar E. Gaggiotti, Andrea Benazzo, Cock Van Oosterhout, Giorgio Bertorelle

Faculty Publications and Other Works -- General Biology

Background

Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable …

Microsyn: A User Friendly Tool For Detection Of Microsynteny In A Gene Family, Bin Cai, Xiaohan Yang, Gerald A. Tusken, Zong-Ming Cheng

Plant Sciences Publications and Other Works

Background

The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.

Results

We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to …

Discovering Gene Functional Relationships Using Faun (Feature Annotation Using Nonnegative Matrix Factorization), Elina Tjioe, Michael W. Berry, Ramin Homayouni

Faculty Publications and Other Works -- EECS

Background

Searching the enormous amount of information available in biomedical literature to extract novel functional relationships among genes remains a challenge in the field of bioinformatics. While numerous (software) tools have been developed to extract and identify gene relationships from biological databases, few effectively deal with extracting new (or implied) gene relationships, a process which is useful in interpretation of discovery-oriented genome-wide experiments.

Results

In this study, we develop a Web-based bioinformatics software environment called FAUN or Feature Annotation Using Nonnegative matrix factorization (NMF) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity …

Comparative Functional Genomic Study Of Substrate Specificity Evolution Of The Sabath Family Of Methyltransferases In Plants, Nan Zhao, Jean-Luc Ferrer, Xiaofeng Zhuang, Feng Chen

Plant Sciences Publications and Other Works

Background

The plant SABATH protein family is composed of a group of related small molecule methyltransferases (MTs) that catalyze the S-adenosyl-L-methionine dependent methylation of a variety of plant small molecular weight metabolites encompassing widely divergent structures. Some of these substrates are important plant hormones and signaling molecules, such as indole-3-acetic acid (IAA), jasmonic acid (JA) and salicylic acid (SA). Methylating these compounds may have important impacts on plant growth and development. In the previous paper, we presented Indole-3-acetic acid (IAA) methyltransferase (IAMT) as an evolutionarily ancient member of the SABATH family in higher plants. Whether the IAMT exists in less …

Graph Algorithms For Machine Learning: A Case-Control Study Based On Prostate Cancer Populations And High Throughput Transcriptomic Data, Gary L. Rogers, Pablo Moscato, Michael A. Langston

Faculty Publications and Other Works -- EECS

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 …

Serendipitous Discoveries In Microarray Analysis, Sally R. Ellingson, Charles A. Phillips, Randy Glenn, Douglas Swanson, Thomas Ha, Daniel Goldowitz, Michael A. Langston

Faculty Publications and Other Works -- EECS

Background

Scientists are capable of performing very large scale gene expression experiments with current microarray technologies. In order to find significance in the expression data, it is common to use clustering algorithms to group genes with similar expression patterns. Clusters will often contain related genes, such as co-regulated genes or genes in the same biological pathway. It is too expensive and time consuming to test all of the relationships found in large scale microarray experiments. There are many bioinformatics tools that can be used to infer the significance of microarray experiments and cluster analysis.

Materials and methods

In this project …

Reconstructing Generalized Logical Networks Of Transcriptional Regulation In Mouse Brain From Temporal Gene Expression Data, Mingzhou (Joe) Song

Faculty Publications and Other Works -- EECS

Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The prsoblem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from transcriptomic data is addressed. A network reconstruction algorithm was developed that uses statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. The multinomial hypothesis testing-based network reconstruction allows for explicit specification of the false-positive rate, unique from all extant network inference algorithms. The method is superior to dynamic Bayesian network modeling in …

Using A Literature-Based Nmf Model For Discovering Gene Functional Relationships, Elina Tjioe, Michael W. Berry, Ramin Homayouni, Kevin Heinrich

Faculty Publications and Other Works -- General Biology

No abstract provided.

Nfu-Enabled Fasta: Moving Bioinformatics Applications Onto Wide Area Networks, Erich J. Baker, Guan N. Lin, Huadong Liu, Ravi Kosuri

Faculty Publications and Other Works -- General Biology

Abstract

Background

Advances in Internet technologies have allowed life science researchers to reach beyond the lab-centric research paradigm to create distributed collaborations. Of the existing technologies that support distributed collaborations, there are currently none that simultaneously support data storage and computation as a shared network resource, enabling computational burden to be wholly removed from participating clients. Software using computation-enable logistical networking components of the Internet Backplane Protocol provides a suitable means to accomplish these tasks. Here, we demonstrate software that enables this approach by distributing both the FASTA algorithm and appropriate data sets within the framework of a wide area …

Statistical Tools For Transgene Copy Number Estimation Based On Real-Time Pcr, Joshua S. Yuan, Jason N Burris, Nathan R. Stewart, Ayalew Mentewab, C. Neal Stewart

Faculty Publications and Other Works -- General Biology

Background

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination.

Results

Three experimental designs and four data quality control integrated statistical models are …

Modeling Sage Tag Formation And Its Effects On Data Interpretation Within A Bayesian Framework, Michael A. Gilchrist, Hong Qin, Russell Zaretzki

Faculty Publications and Other Works -- General Biology

Abstract

Background

Serial Analysis of Gene Expression (SAGE) is a high-throughput method for inferring mRNA expression levels from the experimentally generated sequence based tags. Standard analyses of SAGE data, however, ignore the fact that the probability of generating an observable tag varies across genes and between experiments. As a consequence, these analyses result in biased estimators and posterior probability intervals for gene expression levels in the transcriptome.

Results

Using the yeast Saccharomyces cerevisiae as an example, we introduce a new Bayesian method of data analysis which is based on a model of SAGE tag formation. Our approach incorporates the variation …

Statistical Analysis Of Real-Time Pcr Data, Joshua S. Yuan, Ann Reed, Feng Chen, C. Neal Stewart

Faculty Publications and Other Works -- General Biology

Background

Even though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of appropriate statistical treatment. Confidence interval and statistical significance considerations are not explicit in many of the current data analysis approaches. Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data.

Results

In the first approach, a multiple regression analysis model was developed to derive ΔΔCt from estimation of interaction of gene and …

An Svd-Based Comparison Of Nine Whole Eukaryotic Genomes Supports A Coelomate Rather Than Ecdysozoan Lineage, Gary W. Stuart, Michael W. Berry

Faculty Publications and Other Works -- General Biology

Background

Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putative orthologs in order to reduce the effective size of the dataset and provide a reasonably high but unknown fraction of correctly aligned homologous sites for comparison. As an alternative, highly efficient methods that do not require the pre-alignment of operationally defined orthologs are also being explored.

Results

A non-alignment method based on the Singular …