scholarly journals Comparison of Microarrays and RNA-Seq for Gene Expression Analyses of Dose-Response Experiments

2013 ◽  
Vol 137 (2) ◽  
pp. 385-403 ◽  
Author(s):  
Michael B. Black ◽  
Bethany B. Parks ◽  
Linda Pluta ◽  
Tzu-Ming Chu ◽  
Bruce C. Allen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dose Response ◽  
Rna Seq ◽  
Gene Expression Analyses

scholarly journals Transcriptome Analysis of Marchantin Biosynthesis from the Liverwort Marchantia polymorpha

2017 ◽  
Vol 12 (8) ◽  
pp. 1934578X1701200
Author(s):  
Hironobu Takahashi ◽  
Yoshinori Asakawa
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Transcriptome Sequencing ◽  
Biological Activities ◽  
Digital Gene Expression ◽  
Marchantia Polymorpha ◽  
Rna Seq ◽  
Gene Expression Analyses

Marchantin A, the first characterized macrocyclic bis(bibenzyls) found in the liverwort Marchantia polymorpha shows interesting biological activities such as antifungal, antimicrobial, cytotoxic, antioxidant and muscle relaxing activity. Previously, Zenk et al. reported the phenylpropane/polymalonate pathway in the biosynthesis of the marchantins in M. polymorpha. To clear this pathway, transcriptome sequencing and digital gene expression analyses of M. polymorpha were carried out by using Illumina RNA-seq system.

scholarly journals A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 89 ◽  
Author(s):  
Sheng-Kai Hsu ◽  
Ana Marija Jakšić ◽  
Viola Nolte ◽  
Neda Barghi ◽  
François Mallard ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abiotic Factors ◽  
Transcript Abundance ◽  
Age Difference ◽  
Rna Seq ◽  
Experimental Conditions ◽  
Gene Expression Analyses ◽  
High Throughput Phenotyping ◽  
Influence Gene Expression ◽  
Developmental Staging

Gene expression profiling is one of the most reliable high-throughput phenotyping methods, allowing researchers to quantify the transcript abundance of expressed genes. Because many biotic and abiotic factors influence gene expression, it is recommended to control them as tightly as possible. Here, we show that a 24 h age difference of Drosophila simulans females that were subjected to RNA sequencing (RNA-Seq) five and six days after eclosure resulted in more than 2000 differentially expressed genes. This is twice the number of genes that changed expression during 100 generations of evolution in a novel hot laboratory environment. Importantly, most of the genes differing in expression due to age introduce false positives or negatives if an adaptive gene expression analysis is not controlled for age. Our results indicate that tightly controlled experimental conditions, including precise developmental staging, are needed for reliable gene expression analyses, in particular in an evolutionary framework.

scholarly journals KnowSeq R/bioc package: Beyond the traditional RNA-seq pipeline. A breast cancer case study.

2019 ◽  
Author(s):  
Daniel Castillo-Secilla ◽  
Juan Manuel Galvez ◽  
Francisco Manuel Ortuno ◽  
Luis Javier Herrera ◽  
Ignacio Rojas
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Breast Cancer Case ◽  
Quality Analysis ◽  
Cancer Case ◽  
Biological Knowledge ◽  
Real Problem ◽  
Rna Seq ◽  
Paired Samples ◽  
Gene Expression Analyses

Abstract The number of gene expression analyses has grown exponentially over the last years. The main triggers of this increase are the reduction in the sequencing cost per sample and the technological advances, specially in the computing scope. Those analyses generally involve a number of steps. Firstly, a raw samples alignment and a quality analysis are needed. After that, a Differentially Expressed Genes (DEGs) extraction and a subsequent gene enrichment can be performed. The development of intelligent predictive tools results essential in bioinformatics given that there exists a real need of assistance for decision-making systems towards precision medicine. Therefore, KnowSeq incorporates novel steps of feature selection and classifier design in the traditional RNA-seq pipeline. No tool exists in the research community that achieves this complete RNA-seq analysis, encapsulating all those steps in one single tool. In order to show the functionalities provided by the general pipeline designed for the KnowSeq package, an application to a real problem is presented. Concretely, an analysis of a breast cancer set of patients collected from the controlled repository GDC portal is performed, keeping paired samples between tumour and control. As results show, KnowSeq achieves extracting more relevant biological knowledge related with breast cancer from the RNA raw data acquisition. KnowSeq is available through Bioconductor. KnowSeq R/bioc package is born with the purpose of providing an integrative tool, containing the necessary steps to address complex RNA-seq analyses in a modular and flexible way. In this paper a breast study case is addressed with KnowSeq, obtaining outstanding results and demonstrating the validity of KnowSeq to carry out gene expression analyses.

scholarly journals Differential gene expression analyses related to fruit yield of Jatropha curcas L. using RNA-seq

2018 ◽  
Vol 32 (5) ◽  
pp. 1126-1133
Author(s):  
Wenkai Hui ◽  
Yuantong Yang ◽  
Guojiang Wu ◽  
Yi Wang ◽  
Mohamed Zaky Zayed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Jatropha Curcas ◽  
Fruit Yield ◽  
Rna Seq ◽  
Jatropha Curcas L ◽  
Gene Expression Analyses ◽  
Differential Gene

scholarly journals Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 665
Author(s):  
Hui Yu ◽  
Yan Guo ◽  
Jingchun Chen ◽  
Xiangning Chen ◽  
Peilin Jia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Focal Adhesion ◽  
Biological Pathways ◽  
Postmortem Brain ◽  
Rna Seq ◽  
Hub Genes ◽  
Differential Coexpression ◽  
Pathway Crosstalk ◽  
Microarray Datasets ◽  
Transcriptomic Studies

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or inter-coordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired pathways, were highly mutually consistent among the five datasets. The combinatory list of 92 hub genes was generally multi-functional, suggesting their complex and dynamic roles in SCZ pathophysiology. In our constructed pathway crosstalk network, we found “Clostridium neurotoxicity” and “signaling events mediated by focal adhesion kinase” had the highest interactions. We further identified disconnected gene links underlying the disrupted pathway crosstalk. Among them, four gene pairs (PAK1:SYT1, PAK1:RFC5, DCTN1:STX1A, and GRIA1:MAP2K4) were normally correlated in universal contexts. In summary, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and critical genes and gene links in schizophrenia transcriptomes.

scholarly journals Mitochondrial Mistranslation in Brain Provokes a Metabolic Response Which Mitigates the Age-Associated Decline in Mitochondrial Gene Expression

2021 ◽  
Vol 22 (5) ◽  
pp. 2746
Author(s):  
Dimitri Shcherbakov ◽  
Reda Juskeviciene ◽  
Adrián Cortés Sanchón ◽  
Margarita Brilkova ◽  
Hubert Rehrauer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Response ◽  
Mitochondrial Gene ◽  
Tca Cycle ◽  
Brain Mitochondria ◽  
Mitochondrial Gene Expression ◽  
Rna Seq ◽  
The Tca Cycle ◽  
Neurological Phenotype

Mitochondrial misreading, conferred by mutation V338Y in mitoribosomal protein Mrps5, in-vivo is associated with a subtle neurological phenotype. Brain mitochondria of homozygous knock-in mutant Mrps5V338Y/V338Y mice show decreased oxygen consumption and reduced ATP levels. Using a combination of unbiased RNA-Seq with untargeted metabolomics, we here demonstrate a concerted response, which alleviates the impaired functionality of OXPHOS complexes in Mrps5 mutant mice. This concerted response mitigates the age-associated decline in mitochondrial gene expression and compensates for impaired respiration by transcriptional upregulation of OXPHOS components together with anaplerotic replenishment of the TCA cycle (pyruvate, 2-ketoglutarate).

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