scholarly journals W17. COMPUTATIONAL ANALYSIS OF GENOME-WIDE EXPRESSION STUDIES OF THE EFFECTS OF PHYSICAL EXERCISE IN HUMANS: IMPLICATIONS FOR MENTAL HEALTH

2021 ◽  
Vol 51 ◽  
pp. e156
Author(s):  
Carlos Orozco ◽  
Yeimy González-Giraldo ◽  
Diego A. Bonilla ◽  
Diego A. Forero
Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 492 ◽  
Author(s):  
Buchberger ◽  
Reis ◽  
Lu ◽  
Posnien

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.


2003 ◽  
Vol 55 (2) ◽  
pp. 399-409 ◽  
Author(s):  
Arvind A. Bhagwat ◽  
Ravindra P. Phadke ◽  
David Wheeler ◽  
Sagar Kalantre ◽  
Mohanram Gudipati ◽  
...  

2021 ◽  
Vol 22 (4) ◽  
pp. 2040 ◽  
Author(s):  
Beatriz Sánchez-Parra ◽  
Marta-Marina Pérez-Alonso ◽  
Paloma Ortiz-García ◽  
José Moya-Cuevas ◽  
Mathias Hentrich ◽  
...  

The major auxin, indole-3-acetic acid (IAA), is associated with a plethora of growth and developmental processes including embryo development, expansion growth, cambial activity, and the induction of lateral root growth. Accumulation of the auxin precursor indole-3-acetamide (IAM) induces stress related processes by stimulating abscisic acid (ABA) biosynthesis. How IAM signaling is controlled is, at present, unclear. Here, we characterize the ami1rooty double mutant, that we initially generated to study the metabolic and phenotypic consequences of a simultaneous genetic blockade of the indole glucosinolate and IAM pathways in Arabidopsisthaliana. Our mass spectrometric analyses of the mutant revealed that the combination of the two mutations is not sufficient to fully prevent the conversion of IAM to IAA. The detected strong accumulation of IAM was, however, recognized to substantially impair seed development. We further show by genome-wide expression studies that the double mutant is broadly affected in its translational capacity, and that a small number of plant growth regulating transcriptional circuits are repressed by the high IAM content in the seed. In accordance with the previously described growth reduction in response to elevated IAM levels, our data support the hypothesis that IAM is a growth repressing counterpart to IAA.


Genomics ◽  
2021 ◽  
Vol 113 (2) ◽  
pp. 669-680
Author(s):  
Yeimy González-Giraldo ◽  
Diego A. Forero ◽  
George E. Barreto ◽  
Andrés Aristizábal-Pachón

2006 ◽  
Vol 61 (3) ◽  
pp. 704-722 ◽  
Author(s):  
John-Paul Vermitsky ◽  
Kelly D. Earhart ◽  
W. Lamar Smith ◽  
Ramin Homayouni ◽  
Thomas D. Edlind ◽  
...  

BMJ Open ◽  
2011 ◽  
Vol 1 (1) ◽  
pp. e000053-e000053 ◽  
Author(s):  
A. K. Kemppinen ◽  
J. Kaprio ◽  
A. Palotie ◽  
J. Saarela

2019 ◽  
Vol 20 (5) ◽  
pp. 325-331 ◽  
Author(s):  
Diego A. Forero

Advances in transcriptomic methods have led to a large number of published Genome- Wide Expression Studies (GWES), in humans and model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, the main features of available software for carrying out meta-analysis of GWES have been reviewed and seven packages from the Bioconductor platform and five packages from the CRAN platform have been described. In addition, nine previously described programs and four online programs are reviewed. Finally, advantages and disadvantages of these available programs and proposed key points for future developments have been discussed.


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