scholarly journals Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
W Walter Lorenz ◽  
Rob Alba ◽  
Yuan-Sheng Yu ◽  
John M Bordeaux ◽  
Marta Simões ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Loblolly Pine ◽  
Gene Networks ◽  
Scale Free ◽  
Free Gene

scholarly journals Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms

2009 ◽  
Vol 6 (41) ◽  
pp. 1233-1245 ◽  
Author(s):  
P. Gerlee ◽  
T. Lundh ◽  
B. Zhang ◽  
A. R. A. Anderson
Keyword(s):  
Gene Function ◽  
Degree Distribution ◽  
Gene Networks ◽  
Preferential Attachment ◽  
Bipartite Network ◽  
Scale Free ◽  
Evolving Systems ◽  
Digital Organisms ◽  
Free Gene ◽  
Function Network

We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform A vida . The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with A vida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.

Use of Microarray Analysis to Unveil Transcription Factor and Gene Networks Contributing to β Cell Dysfunction and Apoptosis

2003 ◽  
Vol 1005 (1) ◽  
pp. 55-74 ◽  
Author(s):  
DECIO L. EIZIRIK ◽  
BURAK KUTLU ◽  
JOANNE RASSCHAERT ◽  
MARTINE DARVILLE ◽  
ALESSANDRA K. CARDOZO
Keyword(s):  
Transcription Factor ◽  
Microarray Analysis ◽  
Gene Networks ◽  
Β Cell ◽  
Cell Dysfunction

scholarly journals Period Doubling Bifurcations in a Forced Cell-Free Genetic Oscillator

2021 ◽  
Author(s):  
Lukas Aufinger ◽  
Johann Brenner ◽  
Friedrich C Simmel
Keyword(s):  
Gene Networks ◽  
Computational Models ◽  
Expression System ◽  
Period Doubling ◽  
Genetic Oscillator ◽  
A Cell ◽  
Free Gene ◽  
Favorable Conditions ◽  
Period Doubling Bifurcations ◽  
Good Agreement

Complex non-linear dynamics such as period doubling and chaos have been previously found in computational models of the oscillatory gene networks of biological circadian clocks, but their experimental study is difficult. Here, we present experimental evidence of period doubling in a forced synthetic genetic oscillator operated in a cell-free gene expression system. To this end, an oscillatory negative feedback gene circuit is established in a microfluidic reactor, which allows continuous operation of the system over extended periods of time. We first thoroughly characterize the unperturbed oscillator and find good agreement with a four-species ODE model of the system. Guided by simulations, microfluidics is then used to periodically perturb the system by modulating the concentration of one of the oscillator components with a given amplitude and frequency. When the ratio of the external `zeitgeber' period and the intrinisic period is close to 1, we experimentally find period doubling and quadrupling in the oscillator dynamics, whereas for longer zeitgeber periods, we find stable entrainment. Our theoretical model suggests favorable conditions for which the oscillator can be utilized as an externally synchronized clock, but also demonstrates that related systems could, in principle, display chaotic dynamics.

scholarly journals Identification of New Key Genes in Breast Cancer by Co-expression Network Analysis

2020 ◽  
Author(s):  
Xinyang Li ◽  
Yukun Wang ◽  
Ziming Wang ◽  
Ge Yao ◽  
Jiahao Fan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Network Analysis ◽  
Gene Expression Omnibus ◽  
Oxidoreductase Activity ◽  
Scale Free ◽  
Software Analysis ◽  
Normal Tissues ◽  
Human Protein Atlas ◽  
Free Gene

Abstract Background: Breast cancer is one of the most common malignancies in women all over the world. This study aimed to identify the potential biomarkers associated with the occurrence and development of breast cancer.Results: Our research downloaded GSE54140 gene expression datasets and GPL10152 platform information from the Gene Expression Omnibus datasets, and used weighted gene co-expression network analysis (WGCNA) to construct a scale-free gene co-expression network to explore the associations between gene sets and clinical features. A total of 60 modules were analyzed, and found that the skyblue3 module was significantly related to HER2+ BC. The function of 93 genes in the skyblue3 module was annotated by DAVID bioinformatics tool, and it was demonstrated that the function of the module was mainly related to nuclear-transcribed mRNA catabolic process, cytosol, and oxidoreductase activity. Based on the WGCNA and Cytoscape software analysis, 9 hub genes (PGAP3, PPP1R1B, PNMT, ERBB2, CISD3, CRKRS, TCAP, STARD3, and NEUROD2) were identified. The Human Protein Atlas database detected that the protein level of PGAP3, PPP1R1B, PNMT, ERBB2, CISD3, CRKRS, TCAP, and STARD3 gene in tumor tissues was significantly higher than those in normal tissues. And survival analysis shows that PGAP3, PNMT, ERBB2, TCAP, and STARD3 were negatively associated with the overall survival (P < 0.05).Conclusion: A total of 9 candidate biomarkers were identified by comprehensive bioinformatics analysis, among which, the co-expansion of PGAP3 and CRKRS related to ERBB2 may be associated with the occurrence of breast cancer. In addition, PPP1R1B, CRKRS and TCAP are related to drug resistance and adverse reactions in the treatment of breast cancer.

scholarly journals Identification of human metapneumovirus-induced gene networks in airway epithelial cells by microarray analysis

Virology ◽  
2008 ◽  
Vol 374 (1) ◽  
pp. 114-127 ◽  
Author(s):  
X. Bao ◽  
M. Sinha ◽  
T. Liu ◽  
C. Hong ◽  
B.A. Luxon ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Microarray Analysis ◽  
Gene Networks ◽  
Airway Epithelial Cells ◽  
Human Metapneumovirus ◽  
Airway Epithelial

scholarly journals Sigmoid colon mucosal gene expression supports alterations of neuronal signaling in irritable bowel syndrome with constipation

2018 ◽  
Vol 315 (1) ◽  
pp. G140-G157 ◽  
Author(s):  
Elizabeth J. Videlock ◽  
Swapna Mahurkar-Joshi ◽  
Jill M. Hoffman ◽  
Dimitrios Iliopoulos ◽  
Charalabos Pothoulakis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Irritable Bowel Syndrome ◽  
Sigmoid Colon ◽  
Microarray Analysis ◽  
Gene Networks ◽  
Expression Profiles ◽  
Gene Set Enrichment Analysis ◽  
Healthy Controls ◽  
Neuronal Signaling ◽  
Irritable Bowel

Peripheral factors likely play a role in at least a subset of irritable bowel syndrome (IBS) patients. Few studies have investigated mucosal gene expression using an unbiased approach. Here, we performed mucosal gene profiling in a sex-balanced sample to identify relevant signaling pathways and gene networks and compare with publicly available profiling data from additional cohorts. Twenty Rome III+ IBS patients [10 IBS with constipation (IBS-C), 10 IBS with diarrhea (IBS-D), 5 men/women each), and 10 age-/sex-matched healthy controls (HCs)] underwent sigmoidoscopy with biopsy for gene microarray analysis, including differential expression, weighted gene coexpression network analysis (WGCNA), gene set enrichment analysis, and comparison with publicly available data. Expression levels of 67 genes were validated in an expanded cohort, including the above samples and 18 additional participants (6 each of IBS-C, IBS-D, HCs) using NanoString nCounter technology. There were 1,270 differentially expressed genes (FDR < 0.05) in IBS-C vs. HCs but none in IBS or IBS-D vs. HCs. WGNCA analysis identified activation of the cAMP/protein kinase A signaling pathway. Nine of 67 genes were validated by the NanoString nCounter technology (FDR < 0.05) in the expanded sample. Comparison with publicly available microarray data from the Mayo Clinic and University of Nottingham supports the reproducibility of 17 genes from the microarray analysis and three of nine genes validated by nCounter in IBS-C vs. HCs. This study supports the involvement of peripheral mechanisms in IBS-C, particularly pathways mediating neuronal signaling. NEW & NOTEWORTHY Peripheral factors play a role in the pathophysiology of irritable bowel syndrome (IBS), which, to date, has been mostly evident in IBS with diarrhea. Here, we show that sigmoid colon mucosal gene expression profiles differentiate IBS with constipation from healthy controls. These profiling data and analysis of additional cohorts also support the concept that peripheral neuronal pathways contribute to IBS pathophysiology.

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