Dietary Small Molecules and Large-Scale Gene Expression Studies: An Experimental Approach for Understanding their Beneficial Effects on the Development of Malignant and Non-Malignant Proliferative Diseases

2006 ◽  
Vol 13 (13) ◽  
pp. 1481-1489 ◽  
Author(s):  
Devi Mariappan ◽  
Johannes Winkler ◽  
Vijaya Parthiban ◽  
Michael Doss ◽  
Jurgen Hescheler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Molecules ◽  
Large Scale ◽  
Experimental Approach ◽  
Beneficial Effects ◽  
Expression Studies ◽  
Gene Expression Studies

scholarly journals Trisomy 21 and Down syndrome: a short review

2008 ◽  
Vol 68 (2) ◽  
pp. 447-452 ◽  
Author(s):  
CA. Sommer ◽  
F. Henrique-Silva
Keyword(s):  
Gene Expression ◽  
Down Syndrome ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Global Gene Expression ◽  
Short Review ◽  
Complex Disorder ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Chromosome Segments

Even though the molecular mechanisms underlying the Down syndrome (DS) phenotypes remain obscure, the characterization of the genes and conserved non-genic sequences of HSA21 together with large-scale gene expression studies in DS tissues are enhancing our understanding of this complex disorder. Also, mouse models of DS provide invaluable tools to correlate genes or chromosome segments to specific phenotypes. Here we discuss the possible contribution of HSA21 genes to DS and data from global gene expression studies of trisomic samples.

scholarly journals SMART-RDA: A Galaxy Workflow for RNA-Seq Data Analysis

2017 ◽  
Vol 3 (4) ◽  
pp. 186
Author(s):  
Redi Aditama ◽  
Zulfikar Achmad Tanjung ◽  
Widyartini Made Sudania ◽  
Toni Liwang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Analysis Tool ◽  
Rna Seq ◽  
Expression Studies ◽  
Galaxy Server ◽  
Local Facility ◽  
Computational Workflow ◽  
Gene Expression Studies ◽  
Next Generation Sequencing Ngs

<p class="Els-Abstract-text">RNA-seq using the Next Generation Sequencing (NGS) approach is a common technology to analyze large-scale RNA transcript data for gene expression studies. However, an appropriate bioinformatics tool is needed to analyze a large amount of transcriptomes data from RNA-seq experiment. The aim of this study was to construct a system that can be easily applied to analyze RNA-seq data. RNA-seq analysis tool as SMART-RDA was constructed in this study. It is a computational workflow based on Galaxy framework to be used for analyzing RNA-seq raw data into gene expression information. This workflow was adapted from a well-known Tuxedo Protocol for RNA-seq analysis with some modifications. Expression value from each transcriptome was quantitatively stated as Fragments Per Kilobase of exon per Million fragments (FPKM). RNA-seq data of sterile and fertile oil palm (Pisifera) pollens derived from Sequence Read Archive (SRA) NCBI were used to test this workflow in local facility Galaxy server. The results showed that differentially gene expression in pollens might be responsible for sterile and fertile characteristics in palm oil Pisifera.</p><p><strong>Keywords:</strong> FPKM; Galaxy workflow; Gene expression; RNA sequencing.</p>

scholarly journals A cost-effective RNA sequencing protocol for large-scale gene expression studies

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Zhonggang Hou ◽  
Peng Jiang ◽  
Scott A. Swanson ◽  
Angela L. Elwell ◽  
Bao Kim S. Nguyen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Large Scale ◽  
Cost Effective ◽  
Expression Studies ◽  
Gene Expression Studies

scholarly journals RNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts

2009 ◽  
Vol 2 (1) ◽  
pp. 235 ◽  
Author(s):  
Joëlle Vermeulen ◽  
Stefaan Derveaux ◽  
Steve Lefever ◽  
Els De Smet ◽  
Katleen De Preter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Studies ◽  
Gene Expression Studies

The Netherlands Twin Register Biobank: A Resource for Genetic Epidemiological Studies

2010 ◽  
Vol 13 (3) ◽  
pp. 231-245 ◽  
Author(s):  
Gonneke Willemsen ◽  
Eco J. C. de Geus ◽  
Meike Bartels ◽  
C. E. M. Toos van Beijsterveldt ◽  
Andy I. Brooks ◽  
...  
Keyword(s):  
Gene Expression ◽  
The Netherlands ◽  
Large Scale ◽  
Epidemiological Studies ◽  
Urine Samples ◽  
Sample Collection ◽  
Health Lifestyle ◽  
Phenotypic Information ◽  
Expression Studies ◽  
Gene Expression Studies

AbstractIn 2004 the Netherlands Twin Register (NTR) started a large scale biological sample collection in twin families to create a resource for genetic studies on health, lifestyle and personality. Between January 2004 and July 2008, adult participants from NTR research projects were invited into the study. During a home visit between 7:00 and 10:00 am, fasting blood and morning urine samples were collected. Fertile women were bled on day 2–4 of the menstrual cycle, or in their pill-free week. Biological samples were collected for DNA isolation, gene expression studies, creation of cell lines and for biomarker assessment. At the time of blood sampling, additional phenotypic information concerning health, medication use, body composition and smoking was collected. Of the participants contacted, 69% participated. Blood and urine samples were collected in 9,530 participants (63% female, average age 44.4 (SD 15.5) years) from 3,477 families. Lipid profile, glucose, insulin, HbA1c, haematology, CRP, fibrinogen, liver enzymes and creatinine have been assessed. Longitudinal survey data on health, personality and lifestyle are currently available for 90% of all participants. Genome-wide SNP data are available for 3,524 participants, with additional genotyping ongoing. The NTR biobank, combined with the extensive phenotypic information available within the NTR, provides a valuable resource for the study of genetic determinants of individual differences in mental and physical health. It offers opportunities for DNA-based and gene expression studies as well as for future metabolomic and proteomic projects.

scholarly journals A comprehensive rat transcriptome built from large scale RNA-seq-based annotation

2020 ◽  
Vol 48 (15) ◽  
pp. 8320-8331
Author(s):  
Xiangjun Ji ◽  
Peng Li ◽  
James C Fuscoe ◽  
Geng Chen ◽  
Wenzhong Xiao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Significant Influence ◽  
Large Scale ◽  
Expression Patterns ◽  
Model Organism ◽  
Rna Seq ◽  
Disease Mechanisms ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Different Tissues

Abstract The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.

scholarly journals An Interactive Database of Cocaine-Responsive Gene Expression

2002 ◽  
Vol 2 ◽  
pp. 701-706 ◽  
Author(s):  
Willard M. Freeman ◽  
Kathryn E. Dougherty ◽  
Sally E. Vacca ◽  
Kent E. Vrana
Keyword(s):  
Gene Expression ◽  
Drug Abuse ◽  
Large Scale ◽  
Scientific Information ◽  
Mendelian Inheritance ◽  
General Function ◽  
Expression Studies ◽  
Literature Searches ◽  
Gene Expression Studies ◽  
And Behavior

The postgenomic era of large-scale gene expression studies is inundating drug abuse researchers and many other scientists with findings related to gene expression. This information is distributed across many different journals, and requires laborious literature searches. Here, we present an interactive database that combines existing information related to cocaine-mediated changes in gene expression in an easy-to-use format. The database is limited to statistically significant changes in mRNA or protein expression after cocaine administration. The Flash-based program is integrated into a Web page, and organizes changes in gene expression based on neuroanatomical region, general function, and gene name. Accompanying each gene is a description of the gene, links to the original publications, and a link to the appropriate OMIM (Online Mendelian Inheritance in Man) entry. The nature of this review allows for timely modifications and rapid inclusion of new publications, and should help researchers build second-generation hypotheses on the role of gene expression changes in the physiology and behavior of cocaine abuse. Furthermore, this method of organizing large volumes of scientific information can easily be adapted to assist researchers in fields outside of drug abuse.

scholarly journals MiRonTop: mining microRNAs targets across large scale gene expression studies

2010 ◽  
Vol 26 (24) ◽  
pp. 3131-3132 ◽  
Author(s):  
K. Le Brigand ◽  
K. Robbe-Sermesant ◽  
B. Mari ◽  
P. Barbry
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Studies ◽  
Gene Expression Studies
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