Data mining of Gene expression profiles of Saccharomyces cerevisiae in response to mild heat stress response

We chose yeast as a model organism to explore how eukaryotic cells respond to heat stress. This study provides details on the way yeast responds to temperature changes and is therefore an empirical reference for basic cell research and industrial fermentation of yeast. We use the Qlucore Omics Explorer (QOE) bioinformatics software to analyze the gene expression profiles of the heat stress from Gene Expression Omnibus (GEO). Genes and their expression are listed in heat maps, and the gene function is analyzed against the biological processes and pathways. We can find that the expression of genes changed over time after heat stress. Gene expression changed rapidly from 0 min to 60 min after heat shock, and gene expression stabilized between 60 min to 360 min. The yeast cells begin to adjust themselves to the high temperatures in terms of the level of gene expression at about 60 min. In all of the involved pathways and biological processes, those related to ribosome and nucleic acid metabolism declined in about 15?30 min and those related to starch and sucrose increased in the same time frame. Temperature can be a simple way to control the biological processes and pathways of cell.

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Gene Expression Profiles at Moxibustioned Site (ST36): A Microarray Analysis

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2013/890579 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Hai-Yan Yin ◽

Yong Tang ◽

Sheng-Feng Lu ◽

Ling Luo ◽

Jia-Ping Wang ◽

...

Keyword(s):

Gene Expression ◽

Microarray Analysis ◽

Expression Profiles ◽

Alternative Therapy ◽

Gene Expression Profiles ◽

Biological Processes ◽

Physiological Conditions ◽

Pathological Conditions ◽

Molecular Events ◽

Zusanli Acupoint

As a major alternative therapy in Traditional Chinese Medicine, it has been demonstrated that moxibustion could generate a series of molecular events in blood, spleen, and brain, and so forth. However, what would happen at the moxibustioned site remained unclear. To answer this question, we performed a microarray analysis with skin tissue taken from the moxibustioned site also Zusanli acupoint (ST36) where 15-minute moxibustion stimulation was administrated. The results exhibited 145 upregulated and 72 downregulated genes which responded immediately under physiological conditions, and 255 upregulated and 243 downregulated genes under pathological conditions. Interestingly, most of the pathways and biological processes of the differentially expressed genes (DEGs) under pathological conditions get involved in immunity, while those under physiological conditions are involved in metabolism.

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Gene Expression in RET/PTC3 and E7 Transgenic Mouse Thyroids: RET/PTC3 But Not E7 Tumors Are Partial and Transient Models of Human Papillary Thyroid Cancers

Endocrinology ◽

10.1210/en.2008-0531 ◽

2008 ◽

Vol 149 (10) ◽

pp. 5107-5117 ◽

Cited By ~ 14

Author(s):

Agnès Burniat ◽

Ling Jin ◽

Vincent Detours ◽

Natacha Driessens ◽

Jean-Christophe Goffard ◽

...

Keyword(s):

Gene Expression ◽

Fusion Gene ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Human Thyroid ◽

Matrix Remodeling ◽

Biological Processes ◽

Papillary Thyroid ◽

Thyroid Cancers ◽

Transient Models

We studied gene expression profiles in two mouse models of human thyroid carcinoma: the Tg-RET/PTC3 (RP3) and Tg-E7 mice. RP3 fusion gene is the most frequent mutation found in the first wave post-Chernobyl papillary thyroid cancers (PTCs). E7 is an oncoprotein derived from the human papillomavirus 16 responsible for most cervical carcinoma in women. Both transgenic mice develop thyroid hyperplasia followed by solid differentiated carcinoma in older animals. To understand the different steps leading to carcinoma, we analyzed thyroid gene expression in both strains at different ages by microarray technology. Important biological processes were differentially regulated in the two tumor types. In E7 thyroids, cell cycle was the most up-regulated process, an observation consistent with the huge size of these tumors. In RP3 thyroids, contrary to E7 tumors, several human PTC characteristics were observed: overexpression of many immune-related genes, regulation of human PTC markers, up-regulation of EGF-like growth factors and significant regulation of angiogenesis and extracellular matrix remodeling-related genes. However, similarities were incomplete; they did not concern the overall gene expression and were not conserved in old animals. Therefore, RP3 tumors are partial and transient models of human PTC. They constitute a good model, especially in young animals, to study the respective role of the biological processes shared with human PTC and will allow testing drugs targeting these validated variables.

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Gene expression profiles displayed by peripheral blood mononuclear cells from patients with type 2 diabetes mellitus focusing on biological processes implicated on the pathogenesis of the disease

Gene ◽

10.1016/j.gene.2012.09.090 ◽

2012 ◽

Vol 511 (2) ◽

pp. 151-160 ◽

Cited By ~ 33

Author(s):

Fernanda S. Manoel-Caetano ◽

Danilo J. Xavier ◽

Adriane F. Evangelista ◽

Paula Takahashi ◽

Cristhianna V. Collares ◽

...

Keyword(s):

Gene Expression ◽

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Mononuclear Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Biological Processes ◽

Peripheral Blood Mononuclear ◽

Blood Mononuclear Cells

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Transcriptional Repression by the Pho4 Transcription Factor Controls the Timing of SNZ1 Expression

Eukaryotic Cell ◽

10.1128/ec.00366-07 ◽

2008 ◽

Vol 7 (6) ◽

pp. 949-957 ◽

Cited By ~ 8

Author(s):

Masafumi Nishizawa ◽

Tae Komai ◽

Nobuyuki Morohashi ◽

Mitsuhiro Shimizu ◽

Akio Toh-e

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcriptional Repression ◽

Structural Changes ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Nutrient Sensing ◽

Yeast Cells ◽

Diauxic Shift

ABSTRACT Nutrient-sensing kinases play important roles for the yeast Saccharomyces cerevisiae to adapt to new nutrient conditions when the nutrient status changes. Our previous global gene expression analysis revealed that the Pho85 kinase, one of the yeast nutrient-sensing kinases, is involved in the changes in gene expression profiles when yeast cells undergo a diauxic shift. We also found that the stationary phase-specific genes SNZ1 and SNO1, whch share a common promoter, are not properly induced when Pho85 is absent. To examine the role of the kinase in SNZ1/SNO1 regulation, we analyzed their expression during the growth of various yeast mutants, including those affecting Pho85 function or lacking the Pho4 transcription factor, an in vivo substrate of Pho85, and tested Pho4 binding by chromatin immunoprecipitation. Pho4 exhibits temporal binding to the SNZ1/SNO1 promoter to down-regulate the promoter activity, and a Δpho4 mutation advances the timing of SNZ1/SNO1 expression. SNZ2, another member of the SNZ/SNO family, is expressed at an earlier growth stage than SNZ1, and Pho4 does not affect this timing, although Pho85 is required for SNZ2 expression. Thus, Pho4 appears to regulate the different timing of the expression of the SNZ/SNO family members. Pho4 binding to the SNZ1/SNO1 promoter is accompanied by alterations in chromatin structure, and Rpd3 histone deacetylase is required for the proper timing of SNZ1/SNO1 expression, while Asf1 histone chaperone is indispensable for their expression. These results imply that Pho4 plays positive and negative roles in transcriptional regulation, with both cases involving structural changes in its target chromatin.

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Global Gene Expression Analysis of Yeast Cells during Sake Brewing

Applied and Environmental Microbiology ◽

10.1128/aem.01097-06 ◽

2006 ◽

Vol 72 (11) ◽

pp. 7353-7358 ◽

Cited By ~ 64

Author(s):

Hong Wu ◽

Xiaohong Zheng ◽

Yoshio Araki ◽

Hiroshi Sahara ◽

Hiroshi Takagi ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Global Gene Expression ◽

Yeast Cells ◽

Yeast Gene ◽

High Concentration ◽

Brewing Process ◽

Global Gene Expression Analysis

ABSTRACT During the brewing of Japanese sake, Saccharomyces cerevisiae cells produce a high concentration of ethanol compared with other ethanol fermentation methods. We analyzed the gene expression profiles of yeast cells during sake brewing using DNA microarray analysis. This analysis revealed some characteristics of yeast gene expression during sake brewing and provided a scaffold for a molecular level understanding of the sake brewing process.

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Dynamic Clustering of Gene Expression

ISRN Bioinformatics ◽

10.5402/2012/537217 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12 ◽

Cited By ~ 8

Author(s):

Lingling An ◽

R. W. Doerge

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Optimal Number ◽

Sequential Data ◽

Dynamic Clustering ◽

Biological Processes ◽

Time Frequency ◽

Expression Of Genes

It is well accepted that genes are simultaneously involved in multiple biological processes and that genes are coordinated over the duration of such events. Unfortunately, clustering methodologies that group genes for the purpose of novel gene discovery fail to acknowledge the dynamic nature of biological processes and provide static clusters, even when the expression of genes is assessed across time or developmental stages. By taking advantage of techniques and theories from time frequency analysis, periodic gene expression profiles are dynamically clustered based on the assumption that different spectral frequencies characterize different biological processes. A two-step cluster validation approach is proposed to statistically estimate both the optimal number of clusters and to distinguish significant clusters from noise. The resulting clusters reveal coordinated coexpressed genes. This novel dynamic clustering approach has broad applicability to a vast range of sequential data scenarios where the order of the series is of interest.

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Gene expression profiles during short-term heat stress; branchingvs.massive Scleractinian corals of the Red Sea

PeerJ ◽

10.7717/peerj.1814 ◽

2016 ◽

Vol 4 ◽

pp. e1814 ◽

Cited By ~ 14

Author(s):

Keren Maor-Landaw ◽

Oren Levy

Keyword(s):

Gene Expression ◽

Heat Stress ◽

Redox Regulation ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Marker Genes ◽

Stylophora Pistillata ◽

Stress Genes

It is well-established that there is a hierarchy of susceptibilities amongst coral genera during heat-stress. However, molecular mechanisms governing these differences are still poorly understood. Here we explored if specific corals possessing different morphologies and different susceptibilities to heat stress may manifest varied gene expression patterns. We examined expression patterns of seven genes in the branching coralsStylophora pistillataandAcropora eurystomaand additionally in the massive robust coral,Poritessp. The tested genes are representatives of key cellular processes occurring during heat-stress in Cnidaria: oxidative stress, ER stress, energy metabolism, DNA repair and apoptosis. Varied response to the heat-stress, in terms of visual coral paling, algal maximum quantum yield and host gene expression was evident in the different growth forms. The two branching corals exhibited similar overall responses that differed from that of the massive coral.A. eurystomathat is considered as a susceptible species did not bleach in our experiment, but tissue sloughing was evident at 34 °C. Interestingly, in this species redox regulation genes were up-regulated at the very onset of the thermal challenge. InS. pistillata, bleaching was evident at 34 °C and most of the stress markers were already up-regulated at 32 °C, either remaining highly expressed or decreasing when temperatures reached 34 °C. The massivePoritesspecies displayed severe bleaching at 32 °C but stress marker genes were only significantly elevated at 34 °C. We postulate that by expelling the algal symbionts fromPoritestissues, oxidation damages are reduced and stress genes are activated only at a progressed stage. The differential gene expression responses exhibited here can be correlated with the literature well-documented hierarchy of susceptibilities amongst coral morphologies and genera in Eilat’s coral reef.

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Social boldness correlates with brain gene expression in male green anoles

10.1101/2021.01.15.426859 ◽

2021 ◽

Author(s):

David Kabelik ◽

Allison R. Julien ◽

Dave Ramirez ◽

Lauren A. O’Connell

Keyword(s):

Gene Expression ◽

Social Behavior ◽

Expression Profiles ◽

Coping Styles ◽

Model Organism ◽

Gene Expression Profiles ◽

Ventromedial Hypothalamus ◽

Group Differences ◽

Significant Group ◽

Neural Underpinnings

AbstractWithin populations, some individuals tend to exhibit a bold or shy social behavior phenotype relative to the mean. The neural underpinnings of these differing phenotypes – also described as syndromes, personalities, and coping styles – is an area of ongoing investigation. Although a social decision-making network has been described across vertebrate taxa, most studies examining activity within this network do so in relation to exhibited differences in behavioral expression. Our study instead focuses on constitutive gene expression in bold and shy individuals by isolating baseline gene expression profiles that influence social boldness predisposition, rather than those reflecting the results of social interaction and behavioral execution. We performed this study on male green anole lizards (Anolis carolinensis), an established model organism for behavioral research, which provides a crucial comparison group to investigations of birds and mammals. After identifying subjects as bold or shy through repeated reproductive and agonistic behavior testing, we used RNA sequencing to compare gene expression profiles between these groups within various forebrain, midbrain, and hindbrain regions. The ventromedial hypothalamus had the largest group differences in gene expression, with bold males having increased expression of calcium channels and neuroendocrine receptor genes compared to shy males. Conversely, shy males express more integrin alpha-10 in the majority of examined regions. There were no significant group differences in physiology or hormone levels. Our results highlight the ventromedial hypothalamus as an important center of behavioral differences across individuals and provide novel candidates for investigation into the regulation of individual variation in social behavior phenotype.

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ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

Nucleic Acids Research ◽

10.1093/nar/gkz955 ◽

2019 ◽

Cited By ~ 3

Author(s):

Justine Dardaillon ◽

Delphine Dauga ◽

Paul Simion ◽

Emmanuel Faure ◽

Takeshi A Onuma ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Model Organism ◽

Gene Expression Profiles ◽

Sister Group ◽

Model Organism Database ◽

Oikopleura Dioica ◽

Genetic Features ◽

Taxonomic Range ◽

Or Gene

Abstract ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.

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