Metals and methylotrophy: Via global gene expression studies

2021 ◽  
Author(s):  
Zachary D. Johnson ◽  
Dennis D. Krutkin ◽  
Pavlo Bohutskyi ◽  
Marina G. Kalyuzhnaya
Keyword(s):  
Gene Expression ◽  
Global Gene Expression ◽  
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 Pathway-Level Information ExtractoR (PLIER) for gene expression data

2017 ◽  
Author(s):  
Weiguang Mao ◽  
Elena Zaslavsky ◽  
Boris M. Hartmann ◽  
Stuart C. Sealfon ◽  
Maria Chikina
Keyword(s):  
Gene Expression ◽  
Global Gene Expression ◽  
Expression Data ◽  
Regulate Gene Expression ◽  
Expression Studies ◽  
Inference Algorithms ◽  
Biological Insight ◽  
Level Information ◽  
Gene Expression Studies ◽  
Cell Proportion

AbstractA major challenge in gene expression analysis is to accurately infer relevant biological insight, such as regulation of cell type proportion or pathways, from global gene expression studies. We present a general solution for this problem that outperforms available cell proportion inference algorithms, and is more widely useful to automatically identify specific pathways that regulate gene expression. Our method improves replicability and biological insight when applied to trans-eQTL identification.

scholarly journals Assessment of common housekeeping genes as reference for gene expression studies using RT-qPCR in mouse choroid plexus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kim Hoa Ho ◽  
Annarita Patrizi
Keyword(s):  
Gene Expression ◽  
Choroid Plexus ◽  
Sensory Deprivation ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Experimental Conditions ◽  
Brain Repair ◽  
Expression Studies ◽  
Testing Algorithms ◽  
Gene Expression Studies

AbstractChoroid plexus (ChP), a vascularized secretory epithelium located in all brain ventricles, plays critical roles in development, homeostasis and brain repair. Reverse transcription quantitative real-time PCR (RT-qPCR) is a popular and useful technique for measuring gene expression changes and also widely used in ChP studies. However, the reliability of RT-qPCR data is strongly dependent on the choice of reference genes, which are supposed to be stable across all samples. In this study, we validated the expression of 12 well established housekeeping genes in ChP in 2 independent experimental paradigms by using popular stability testing algorithms: BestKeeper, DeltaCq, geNorm and NormFinder. Rer1 and Rpl13a were identified as the most stable genes throughout mouse ChP development, while Hprt1 and Rpl27 were the most stable genes across conditions in a mouse sensory deprivation experiment. In addition, Rpl13a, Rpl27 and Tbp were mutually among the top five most stable genes in both experiments. Normalisation of Ttr and Otx2 expression levels using different housekeeping gene combinations demonstrated the profound effect of reference gene choice on target gene expression. Our study emphasized the importance of validating and selecting stable housekeeping genes under specific experimental conditions.

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