scholarly journals NCR-PCOPGene: An Exploratory Tool for Analysis of Sample-Classes Effect on Gene-Expression Relationships

2008 ◽  
Vol 2008 ◽  
pp. 1-7
Author(s):  
Juan Cedano ◽  
Mario Huerta ◽  
Enrique Querol
Keyword(s):  
Gene Expression ◽  
Web Application ◽  
Biological Information ◽  
Microarray Technology ◽  
Previous Knowledge ◽  
Type B ◽  
Gene Expressions ◽  
Microarray Experiments ◽  
Maximum Value ◽  
Class Definition

Background. Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data. Our tools allow researchers to test and formulate from a hypothesis to entire models. Results. The objective of the NCRPCOPGene is to study the relationships among gene expressions under different conditions, to classify these conditions, and to study their effect on the different relationships. The web application makes it easier to define the sample classes, grouping the microarray experiments either by using (a) biological, statistical, or any other previous knowledge or (b) their effect on the expression relationship maintained among specific genes of interest. By means of the type (a) class definition, the researcher can add biological information to the gene-expression relationships. The type (b) class definition allows for linking genes correlated neither linearly nor nonlinearly. Conclusions. The PCOPGene tools are especially suitable for microarrays with large sample series. This application helps to identify cellular states and the genes involved in it in a flexible way. The application takes advantage of the ability of our system to relate gene expressions; even when these relationships are noncontinuous and cannot be found using linear or nonlinear analytical methods.

Microarray analysis of the transcriptome of the subfornical organ in the rat: regulation by fluid and food deprivation

2008 ◽  
Vol 295 (6) ◽  
pp. R1914-R1920 ◽  
Author(s):  
Charles Hindmarch ◽  
Mark Fry ◽  
Song T. Yao ◽  
Pauline M. Smith ◽  
David Murphy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Statistical Analysis ◽  
Food Deprivation ◽  
Subfornical Organ ◽  
Microarray Technology ◽  
Type B ◽  
Bdnf Expression ◽  
Experimental Conditions ◽  
Calcium Sensing ◽  
First Time

We have employed microarray technology using Affymetrix 230 2.0 genome chips to initially catalog the transcriptome of the subfornical organ (SFO) under control conditions and to also evaluate the changes (common and differential) in gene expression induced by the challenges of fluid and food deprivation. We have identified a total of 17,293 genes tagged as present in one of our three experimental conditions, transcripts, which were then used as the basis for further filtering and statistical analysis. In total, the expression of 46 genes was changed in the SFO following dehydration compared with control animals (22 upregulated and 24 downregulated), with the largest change being the greater than fivefold increase in brain-derived neurotrophic factor (BDNF) expression, while significant changes in the expression of the calcium-sensing (upregulated) and apelin (downregulated) receptors were also reported. In contrast, food deprivation caused greater than twofold changes in a total of 687 transcripts (222 upregulated and 465 downregulated), including significant reductions in vasopressin, oxytocin, promelanin concentrating hormone, cocaine amphetamine-related transcript (CART), and the endothelin type B receptor, as well as increases in the expression of the GABAB receptor. Of these regulated transcripts, we identified 37 that are commonly regulated by fasting and dehydration, nine that were uniquely regulated by dehydration, and 650 that are uniquely regulated by fasting. We also found five transcripts that were differentially regulated by fasting and dehydration including BDNF and CART. In these studies we have for the first time described the transcriptome of the rat SFO and have in addition identified genes, the expression of which is significantly modified by either water or food deprivation.

DNA Microarrays in Otolaryngology-Head and Neck Surgery

2002 ◽  
Vol 127 (3) ◽  
pp. 196-204 ◽  
Author(s):  
Mark Eliot Whipple ◽  
Winston Patrick Kuo
Keyword(s):  
Gene Expression ◽  
Head And Neck ◽  
Dna Microarrays ◽  
Clinical Medicine ◽  
Neck Surgery ◽  
Head And Neck Surgery ◽  
Microarray Technology ◽  
Single Experiment ◽  
Substantial Impact ◽  
Microarray Experiments

OBJECTIVES: Our goal was to review the technologies underlying DNA microarrays and to explore their use in otolaryngology-head and neck surgery. STUDY DESIGN: The current literature relating to microarray technology and methodology is reviewed, specifically the use of DNA microarrays to characterize gene expression. Bioinformatics involves computational and statistical methods to extract, organize, and analyze the huge amounts of data produced by microarray experiments. The means by which these techniques are being applied to otolaryngology-head and neck surgery are outlined. RESULTS: Microarray technologies are having a substantial impact on biomedical research, including many areas relevant to otolaryngology-head and neck surgery. CONCLUSIONS: DNA microarrays allow for the simultaneous investigationof thousands of individual genes in a single experiment. In the coming years, the application of these technologies to clinical medicine should allow for unprecedented methods ofdiagnosis and treatment. SIGNIFICANCE: These highly parallel experimental techniques promise to revolutionize gene discovery, disease characterization, and drug development.

scholarly journals Gene based Disease Prediction using Pattern Similarity based Classification

2019 ◽  
Vol 8 (11) ◽  
pp. 3223-3227
Keyword(s):  
Gene Expression ◽  
Disease Classification ◽  
Classification Method ◽  
Biological Information ◽  
Accuracy Evaluation ◽  
Gene Expressions ◽  
Single Experiment ◽  
Evaluation Time ◽  
Pattern Similarity ◽  
Gene Data

In today’s biology research in a single experiment scientist can simultaneously measure the expression of levels of thousands of genes. The molecular level of the cell is represented in gene expression profile. And it helps for medical diagnosis tools. For addressing the fundamental harms which helps to diagnosis and discovery gene expression data along with diseases classification is included. Monitoring of large number of gene expressions is possible because of this DNAmicroarray technique. Using this large quantity of gene data, experts are trying to find the probability of disease classification using gene expression dataset. Number of technique has been formed with comfortable results over these years. Still there are issues which need to be address and understood. To overcome this disease classification difficulty, it is required to review at the problem, the related issues and proposed solutions together. This paper presents a comprehensive clustering method and classification method such as Partial Swarm Optimization algorithm, K-NN classification algorithm and estimate them based on theirclassification accuracy,evaluation time and to reveal biological information about genes. Based on our multiclass classification method to diagnosis the diseases and also find severity levels of diseases. Our experimental results show that proposed semi supervised classifier performance improved in accuracy percentage.

Custom microarray for glycobiologists: considerations for glycosyltransferase gene expression profiling

2002 ◽  
Vol 69 ◽  
pp. 135-142 ◽  
Author(s):  
Elena M. Comelli ◽  
Margarida Amado ◽  
Steven R. Head ◽  
James C. Paulson
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Affymetrix Genechip ◽  
Microarray Technology ◽  
Gene Arrays ◽  
Glycosyltransferase Gene

The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip® arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. This chapter describes the main issues related to the establishment of a custom glycogenes array.

Chemoprotective Effects of Propolis on Aflatoxin B1-Induced Hepatotoxicity in Rats: Oxidative Damage and Hepatotoxicity by Modulating TP53, Oxidative Stress

2020 ◽  
Vol 17 (3) ◽  
pp. 191-199
Author(s):  
Seval Yilmaz ◽  
Fatih Mehmet Kandemir ◽  
Emre Kaya ◽  
Mustafa Ozkaraca
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Oxidative Damage ◽  
Aflatoxin B1 ◽  
Tp53 Gene ◽  
Control Group ◽  
Glutathione S Transferase ◽  
Gene Expressions ◽  
Cat Gene ◽  
Gst Activity

Objective: This study aimed to detect hepatic oxidative damage caused by aflatoxin B1 (AFB1), as well as to examine how propolis protects against hepatotoxic effects of AFB1. Method: Rats were split into four groups as control group, AFB1 group, propolis group, AFB1+ propolis group. Results: There was significant increase in malondialdehyde (MDA) level and tumor suppressor protein (TP53) gene expression, Glutathione (GSH) level, Catalase (CAT) activity, CAT gene expression decreased in AFB1 group in blood. MDA level and Glutathione-S-Transferase (GST) activity, GST and TP53 gene expressions increased in AFB1 group, whereas GSH level and CAT activity alongside CAT gene expression decreased in liver. AFB1+propolis group showed significant decrease in MDA level, GST activity, TP53 and GST gene expressions, GSH level and CAT activity and CAT gene expression increased in liver compared to AFB1 group. Conclusion: These results suggest that propolis may potentially be natural agent that prevents AFB1- induced oxidative stress and hepatotoxicity.

scholarly journals Study on browning mechanism of fresh-cut eggplant (Solanum melongena L.) based on metabolomics, enzymatic assays and gene expression

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaohui Liu ◽  
Aidong Zhang ◽  
Jing Shang ◽  
Zongwen Zhu ◽  
Ye Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruits And Vegetables ◽  
Solanum Melongena ◽  
Downward Trend ◽  
Glutathione Metabolism ◽  
Phenylpropanoid Metabolism ◽  
Kegg Pathways ◽  
Maximum Value ◽  
Cut Time ◽  
Fresh Cut

AbstractEnzymatic browning is one of the crucial problems compromising the flavor and texture of fresh-cut fruit and vegetables. In this study, an untargeted metabolomics approach based on liquid chromatography-mass spectrometry (LC–MS) was used to explore the browning mechanism in fresh-cut eggplant. Metabolomics studies showed that with the increase of fresh-cut time, the contents of 946 metabolites changed dynamically. The metabolites having the same trend share common metabolic pathways. As an important browning substrate, the content of chlorogenic acid increased significantly, suggesting that may be more important to fresh-cut eggplant browning; all 119 common differential metabolites in 5 min/CK and 3 min/CK contrastive groups were mapped onto 31 KEGG pathways including phenylpropanol metabolism, glutathione metabolism pathway, et al. In physiological experiments, results showed that the Phenylpropanoid-Metabolism-Related enzymes (PAL, C4H, 4CL) were changed after fresh-cut treatment, the activities of three enzymes increased first and then decreased, and reached the maximum value at 5 min, indicating the accumulation of phenolic substances. At the same time, ROS were accumulated when plant tissue damaged by cutting, the activities of related antioxidant enzymes (SOD, APX and CAT) changed dynamically after oxidative damage. SOD and APX content increased significantly and reached the maximum value at 10 min after cutting, and then showed a downward trend. However, CAT activity increased sharply and reached the maximum value within 3 min after cutting, then maintained the same activity, and showed a downward trend after 30 min. These data fully demonstrated that the activities of browning related enzymes and gene expression increased with the prolonging of fresh cutting time. We explained the browning mechanism of fresh-cut eggplant by combining metabolomics and physiology, which may lay the foundation for better understanding the mechanism of browning during the fruits and vegetables during processing.

scholarly journals Mining The Cancer Genome Atlas gene expression data for lineage markers in distinguishing bladder urothelial carcinoma and prostate adenocarcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ewe Seng Ch’ng
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
The Cancer Genome Atlas ◽  
Relative Importance ◽  
Expression Data ◽  
Gene Expressions ◽  
Urothelial Carcinomas ◽  
Cancer Genome Atlas ◽  
Lineage Markers ◽  
Genome Atlas

AbstractDistinguishing bladder urothelial carcinomas from prostate adenocarcinomas for poorly differentiated carcinomas derived from the bladder neck entails the use of a panel of lineage markers to help make this distinction. Publicly available The Cancer Genome Atlas (TCGA) gene expression data provides an avenue to examine utilities of these markers. This study aimed to verify expressions of urothelial and prostate lineage markers in the respective carcinomas and to seek the relative importance of these markers in making this distinction. Gene expressions of these markers were downloaded from TCGA Pan-Cancer database for bladder and prostate carcinomas. Differential gene expressions of these markers were analyzed. Standard linear discriminant analyses were applied to establish the relative importance of these markers in lineage determination and to construct the model best in making the distinction. This study shows that all urothelial lineage genes except for the gene for uroplakin III were significantly expressed in bladder urothelial carcinomas (p < 0.001). In descending order of importance to distinguish from prostate adenocarcinomas, genes for uroplakin II, S100P, GATA3 and thrombomodulin had high discriminant loadings (> 0.3). All prostate lineage genes were significantly expressed in prostate adenocarcinomas(p < 0.001). In descending order of importance to distinguish from bladder urothelial carcinomas, genes for NKX3.1, prostate specific antigen (PSA), prostate-specific acid phosphatase, prostein, and prostate-specific membrane antigen had high discriminant loadings (> 0.3). Combination of gene expressions for uroplakin II, S100P, NKX3.1 and PSA approached 100% accuracy in tumor classification both in the training and validation sets. Mining gene expression data, a combination of four lineage markers helps distinguish between bladder urothelial carcinomas and prostate adenocarcinomas.

scholarly journals Histochemical Characterisation and Gene Expression Analysis of Skeletal Muscles from Maremmana and Aubrac Steers Reared on Grazing and Feedlot Systems

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 656
Author(s):  
Giulia Foggi ◽  
Francesca Ciucci ◽  
Maria Conte ◽  
Laura Casarosa ◽  
Andrea Serra ◽  
...  
Keyword(s):  
Gene Expression ◽  
Physical Activity ◽  
Muscle Fibre ◽  
Skeletal Muscles ◽  
Gene Expression Analysis ◽  
Type I ◽  
Triceps Brachii ◽  
Gene Expressions ◽  
Muscle Properties ◽  
Voluntary Physical Activity

This study aimed to characterise the fibre composition of Triceps brachii (TB) and Semimembranosus (SM) muscles from 20 Maremmana (MA) and 20 Aubrac (AU) steers, and the effect of grazing activity in comparison with feedlot system. The histochemical method was performed with the m-ATPase method with an acid pre-incubation, thus allowing to distinguish type I, IIA, and IIB fibres. Additionally, on total RNA extracted from SM muscle, the expressions of atp1a1, mt-atp6, and capn1 genes were evaluated, in order to find potential associations with muscle fibre histochemical characteristics. In SM muscle, the MA steers had the greater frequency of oxidative fibres (type I and IIA) and the higher atp1a1 expression, in comparison to AU steers. Conversely, AU steers had a greater frequency of type IIB fibres, and the higher capn1 expression. A similar histochemical pattern was observed in TB muscle. The grazing activity was probably insufficient to determine differences both for fibre proportion and size, and gene expressions, except for mt-atp6 expression that was surprisingly highest in feedlot MA in comparison to other steers. These findings further the knowledge of muscle properties belonging to these breeds, and the effect of voluntary physical activity since few studies were available in this regard.

scholarly journals Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation

2020 ◽  
Vol 14 (1) ◽  
Author(s):  
Fatemeh Khodabandehloo ◽  
Sara Taleahmad ◽  
Reza Aflatoonian ◽  
Farzad Rajaei ◽  
Zahra Zandieh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Wnt Signaling Pathway ◽  
Hub Genes ◽  
Gene Expressions ◽  
Cell Based Therapy ◽  
Wnt Pathways ◽  
Key Pathways

Abstract Background Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs were derived from the three different days compared with day 0. Results Gene expression profiles of GSE37558 were obtained from the Gene Expression Omnibus (GEO) database. A total of 4076 DEGs were acquired on days 8, 12, and 25. Gene ontology (GO) enrichment analysis showed that the non-canonical Wnt signaling pathway and lipopolysaccharide (LPS)-mediated signaling pathway were commonly upregulated DEGs for all 3 days. KEGG pathway analysis indicated that the PI3K-Akt and focal adhesion were also commonly upregulated DEGs for all 3 days. Ten hub genes were identified by CytoHubba on days 8, 12, and 25. Then, we focused on the association of these hub genes with the Wnt pathways that had been enriched from the protein-protein interaction (PPI) by the Cytoscape plugin MCODE. Conclusions These findings suggested further insights into the roles of the PI3K/AKT and Wnt pathways and their association with osteogenesis. In addition, the stem cell microenvironment via growth factors, extracellular matrix (ECM), IGF1, IGF2, LPS, and Wnt most likely affect osteogenesis by PI3K/AKT.

Sign in / Sign up

Export Citation Format

Share Document