scholarly journals Discovering gene expression patterns in time course microarray experiments by ANOVA–SCA

2007 ◽  
Vol 23 (14) ◽  
pp. 1792-1800 ◽  
Author(s):  
María José Nueda ◽  
Ana Conesa ◽  
Johan A. Westerhuis ◽  
Huub C. J. Hoefsloot ◽  
Age K. Smilde ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Microarray Experiments

scholarly journals Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data

2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Qihua Tan ◽  
Mads Thomassen ◽  
Mark Burton ◽  
Kristian Fredløv Mose ◽  
Klaus Ejner Andersen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Correlation Coefficient ◽  
Parametric Analysis ◽  
Time Course ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Microarray Time Course ◽  
Time Course Data ◽  
Generalized Correlation ◽  
Non Parametric

AbstractModeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.

scholarly journals Time Course of Gene Expression during Porphyromonas gingivalis Strain ATCC 33277 Biofilm Formation

2011 ◽  
Vol 77 (18) ◽  
pp. 6733-6736 ◽  
Author(s):  
Reiko Yamamoto ◽  
Yuichiro Noiri ◽  
Mikiyo Yamaguchi ◽  
Yoko Asahi ◽  
Hazuki Maezono ◽  
...  
Keyword(s):  
Gene Expression ◽  
Porphyromonas Gingivalis ◽  
Biofilm Formation ◽  
Time Course ◽  
Growth Stage ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Strain Atcc ◽  
Content Type ◽  
Number Of Genes

ABSTRACTChronological gene expression patterns of biofilm-forming cells are important to understand bioactivity and pathogenicity of biofilms. ForPorphyromonas gingivalisATCC 33277 biofilm formation, the number of genes differentially regulated by more than 1.5-fold was highest during the growth stage (312/2,090 genes), and some pathogen-associated genes were time-dependently controlled.

scholarly journals Time-course transcriptome landscape of achene development in lettuce

2020 ◽  
Author(s):  
Chen Luo ◽  
Shenglin Wang ◽  
Kang Ning ◽  
Zijing Chen ◽  
Jingjing Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Patterns ◽  
Morphological Characteristics ◽  
Gene Expression Patterns ◽  
Biological Processes ◽  
Transcriptome Data ◽  
Development Stages ◽  
Functional Studies ◽  
Lettuce Seeds

AbstractLettuce (Lactuca sativa L.), which belongs to the large Asteraceae (Compositae) family, breeds by sexual reproduction and produce seeds. Actually, lettuce seeds are achenes, which are defined as fruits. However, few studies have described the morphological characteristics of the lettuce achenes, and genes essential for achene development are largely unknown in lettuce. To investigate the gene activity during achene development and determine the possible mechanisms that influence achene development in lettuce, we performed a time-course transcriptome analysis of lettuce achenes. A total of 23,790 expressed genes were detected at the five achene development stages. We investigated the gene expression patterns during achene development and identified the enriched biological processes at the corresponding stages. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed a variety of transcriptomic similarities and differentiation at different achene development stages. Further, transcription factors and phytohormones were found to play important roles during achene development. Finally, we proposed a working model to illustrate the gene expression modules and possible molecular mechanism underlying achene development. Our time-course transcriptome data also provides a foundation for future functional studies to reveal the genetic control of achene development in lettuce.

scholarly journals Time course Analysis of Gene expression patterns in ZebrafIsh Eye during Optic Nerve Regeneration

2010 ◽  
Vol 4 ◽  
pp. JEN.S5006 ◽  
Author(s):  
Amy T. Mccurley ◽  
Gloria V. Callard
Keyword(s):  
Gene Expression ◽  
Optic Nerve ◽  
Nerve Regeneration ◽  
Time Course ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Neural Cells ◽  
Nerve Crush ◽  
Optic Nerve Regeneration

It is well-established that neurons in the adult mammalian central nervous system (CNS) are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX), retinal ganglion cells (RGC) regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ~21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after ONX can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration. To define different phases of regeneration after ONX, alpha tubulin 1 ( tuba1) and growth-associated protein 43 ( gap43), markers previously shown to correspond to morphophological events, were measured by real time quantitative PCR (qPCR). Microarray analysis was then performed at defined intervals (6 hours, 1, 4, 12, and 21 days) post-ONX and compared to SHAM. Results show that optic nerve damage induces multiple, phase-related transcriptional programs, with the maximum number of genes changed and highest fold-change occurring at 4 days. Several functional groups affected by optic nerve regeneration, including cell adhesion, apoptosis, cell cycle, energy metabolism, ion channel activity, and calcium signaling, were identified. Utilizing the whole eye allowed us to identify signaling contributions from the vitreous, immune and glial cells as well as the neural cells of the retina. Comparisons between our dataset and transcriptional profiles from other models of regeneration in zebrafish retina, heart and fin revealed a subset of commonly regulated transcripts, indicating shared mechanisms in different regenerating tissues. Knowledge of gene expression patterns in all components of the eye in a model of successful regeneration provides an entry point for functional analyses, and will help in devising hypotheses for testing normal and toxic regulatory factors.

scholarly journals Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yiming Guan ◽  
Meili Chen ◽  
Yingying Ma ◽  
Zhenglin Du ◽  
Na Yuan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Root Rot ◽  
Time Course ◽  
Expression Patterns ◽  
Defense Responses ◽  
Infection Process ◽  
Ginseng Root ◽  
Gene Expression Patterns ◽  
Rna Seq ◽  
First Time

Abstract Ilyonectria robusta causes rusty root rot, the most devastating chronic disease of ginseng. Here, we for the first time report the high-quality genome of the I. robusta strain CD-56. Time-course (36 h, 72 h, and 144 h) dual RNA-Seq analysis of the infection process was performed, and many genes, including candidate effectors, were found to be associated with the progression and success of infection. The gene expression profile of CD-56 showed a trend of initial inhibition and then gradually returned to a profile similar to that of the control. Analyses of the gene expression patterns and functions of pathogenicity-related genes, especially candidate effector genes, indicated that the stress response changed to an adaptive response during the infection process. For ginseng, gene expression patterns were highly related to physiological conditions. Specifically, the results showed that ginseng defenses were activated by CD-56 infection and persisted for at least 144 h thereafter but that the mechanisms invoked were not effective in preventing CD-56 growth. Moreover, CD-56 did not appear to fully suppress plant defenses, even in late stages after infection. Our results provide new insight into the chronic pathogenesis of CD-56 and the comprehensive and complex inducible defense responses of ginseng root to I. robusta infection.

Gene expression patterns in blood predict future severe endpoints in community acquired pneumonia

Pneumologie ◽  
2018 ◽  
Vol 72 (S 01) ◽  
pp. S8-S9
Author(s):  
M Bauer ◽  
H Kirsten ◽  
E Grunow ◽  
P Ahnert ◽  
M Kiehntopf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Community Acquired Pneumonia ◽  
Gene Expression Patterns
Sign in / Sign up

Export Citation Format

Share Document