Digital Commons Network^™

A Comparison Of Computational Approaches For Intron Retention Detection, Jiantao Zheng, Cuixiang Lin, Zhenpeng Wu, Hong-Dong Li

Big Data Mining and Analytics

Intron Retention (IR) is an alternative splicing mode through which introns are retained in mature RNAs rather than being spliced in most cases. IR has been gaining increasing attention in recent years because of its recognized association with gene expression regulation and complex diseases. Continuous efforts have been dedicated to the development of IR detection methods. These methods differ in their metrics to quantify retention propensity, performance to detect IR events, functional enrichment of detected IRs, and computational speed. A systematic experimental comparison would be valuable to the selection and use of existing methods. In this work, we conduct an …

Classification Of Mild Cognitive Impairment By Fusing Neuroimaging And Gene Expression Data, Yanjun Lyu, Xiaowei Yu, Lu Zhang, Dajiang Zhu

Association of Computing Machinery Open Access Agreement Publications

As reversing the pathology of Alzheimer’s disease (AD) is impossible, the diagnosis of mild cognitive impairment (MCI), which is considered as the precursor of AD, has become a more tractable goal. Because both brain structural and functional alterations have been observed in MCI patients, many multimodal fusion approaches have been proposed to classify MCI from normal controls (NC) in clinical studies. Given the complex relationships between brain structure and function, deep learning based models can be helpful in revealing potential non-linear relationships buried in multimodal neuroimaging data. Meanwhile, RNA expression microarray profile can be a complementary feature in brain diseases …

Degradation Of Transcriptional Repressor Atf4 During Long-Term Synaptic Plasticity, Spencer G. Smith, Kathryn A. Haynes, Ashok N. Hegde

Faculty and Staff Works

Maintenance of long-term synaptic plasticity requires gene expression mediated by cAMP-responsive element binding protein (CREB). Gene expression driven by CREB can commence only if the inhibition by a transcriptional repressor activating transcription factor 4 (ATF4; also known as CREB2) is relieved. Previous research showed that the removal of ATF4 occurs through ubiquitin-proteasome-mediated proteolysis. Using chemically induced hippocampal long-term potentiation (cLTP) as a model system, we investigate the mechanisms that control ATF4 degradation. We observed that ATF4 phosphorylated at serine-219 increases upon induction of cLTP and decreases about 30 min thereafter. Proteasome inhibitor β-lactone prevents the decrease in ATF4. We found …

Computational Approaches For Finding Disease Related Genes And Rnas, Negin Fraidouni

Computer Science and Engineering Dissertations

Finding candidate genes that could cause specific diseases has been the subject of many studies. This is an important research task, however in the biological experimentation domain it can be very expensive and time consuming. So an alternative way is to find gene expression values from partial measurements and try to predict the rest. By using computational methods, we can statistically estimate these relationships faster and in a more efficient way, providing domain experts suggestions on what exploration of likely relationships they should be focusing. One common computational approach is to model the gene expression data as a matrix (where …

Red Drum Diet Exposure To Deepwater Horizon Crude Oil Contaminated Feed: Gene Expression, Dana Wetzel

C-IMAGE data

This dataset contains Ct values and efficiencies of deferentially expressed genes of red drum spleen and liver tissues after exposure via pellets saturated with south Louisiana crude oil for 14 days.

Red Drum Cewaf Uptake/Depuration Study: Immune Function Assays & Gene Expression, Dana Wetzel

C-IMAGE data

Cytokine concentrations in red drum after exposure to chemically enhanced water accommodated fraction (CEWAF) of south Louisiana crude oil. Ct and percent efficiencies of the deferentially expressed genes of red drum spleen, liver and gill tissue exposed to south Louisiana crude oil CEWAF are provided.

Distinct Cardiac Responses To Heat Stress Between Two Broiler Lines Identified By Transcriptome Analysis, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont

Jibin Zhang

Jibin Zhang's Ppt For Midwest Meeting.Pdf, Jibin Zhang, Yeunsu Suh, Young Min Choi, Michael E. Davis, Kichoon Lee

Jibin Zhang