Analysis gene expression. Medical search. Frequent questions

DEGs, or Differentially Expressed Genes, are genes whose expression levels show significant differences between two or more conditions or experimental groups. (pharmiweb.com)
After identifying Differentially Expressed Genes (DEGs), we delve deeper into their functional significance. (pharmiweb.com)
Then they perform supervised analyses to identify differentially methylated or expressed genes. (scientistlive.com)
Using reference distributions for the expression of each human gene in each major leukocyte subtype, we mapped the cellular origin of transcripts found to be differentially expressed in the circulating immune cells from chronically lonely individuals. (nih.gov)
It has become a prevalent technology, allowing an efficient genome-wide relative quantification of gene expression and, in particular, it is the method of choice to find differentially expressed genes between two or more biological conditions of interest. (frontiersin.org)
To identify key genes differentially expressed in the human retinal pigment epithelium (hRPE) following low-level West Nile virus (WNV) infection. (molvis.org)
Our analysis identified five genes (GTF2H2, KLHL5, LRRC37A4P, PRR24, and MRPL23) that were significantly differentially expressed in the tissue of patients with neuropathic pain compared to controls. (iasp-pain.org)
In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)
Estimates using per-gene and common variance ANOVA models indicated that 6-15% of 26,107 genes were differentially expressed between the progenitors. (purdue.edu)
Differentially expressed genes in the polyploids were over-represented by genes differential between the progenitors. (purdue.edu)
By integrating two datasets (GSE77459 and GSE92681) in the GEO database using the sva and limma packages of R, differentially expressed genes (DEGs) of pulpitis were identified. (researchsquare.com)
The OA subchondral bone dataset GSE51588 was downloaded from the GEO database, and the differentially expressed genes (DEGs) were screened. (spandidos-publications.com)
Core genes were expressed differentially between OA subchondral bone and normal tissue samples. (spandidos-publications.com)
The purpose of the study was to identify the key genes that were differentially expressed in these disc cells compared to cells without inflammatory cytokine treatment, using bioinformatics analyses, and to explore the related signaling pathways and interaction networks, providing clues to the molecular mechanisms of disc degeneration for future experimental studies. (minervamedica.it)
4 samples each) were identified using the R language, and were pooled using the Excel software program to select the common differentially expressed genes in the two datasets. (minervamedica.it)
RESULTS: Of the 255 concomitantly and differentially expressed genes identified after respective treatment with TNF-α and IL-1β, 141 were up-regulated and 114 were down-regulated. (minervamedica.it)
The gene ontology annotation analysis showed that these differentially expressed genes were primarily associated with cytokine activity, growth factor activity, the inflammatory reaction and the response to injury. (minervamedica.it)
The signaling pathway analysis showed that these differentially expressed genes were mainly related to the interactions of cytokines, apoptosis and NOD-like receptor signaling pathways. (minervamedica.it)
Biologically, it is not convincing that the top 10,000 genes are differentially expressed. (peerj.com)
In this study, we performed a new bioinformatics analysis on microarray-based gene expression data obtained from the public domain to explore genes that were differentially induced by drugs between the group of capreomycin and PA-824 and the group of mainly the first-line TB drugs. (hindawi.com)

By subjecting DEGs to gene ontology enrichment analysis, pathway analysis, or functional annotation, we gain insights into the biological processes, molecular functions, and pathways associated with the observed gene expression changes. (pharmiweb.com)
We also analyzed the impact of both the replicate number and library size on gene ontology (GO) enrichment analysis. (frontiersin.org)
DAVID was used to perform the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis for the different expression genes (DEGs). (medscimonit.com)
Then, the DEGs were analysed to identify biological pathways of dental pulp inflammation with Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA). (researchsquare.com)
Functional enrichment analysis was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and then Gene Set Enrichment Analysis (GSEA) was used to formulate the molecular functions and pathways based on the results of GO and KEGG analyses. (spandidos-publications.com)
MicroScope is a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network visualization. (biostars.org)
Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. (biomedcentral.com)

A comparative study of public gene-expression data of seven types of cancers (breast, colon, kidney, lung, pancreatic, prostate and stomach cancers) was conducted with the aim of deriving marker genes, along with associated pathways, that are either common to multiple types of cancers or specific to individual cancers. (unl.edu)
By integrating different datasets from the Gene Expression Omnibus (GEO) database, we analysed a merged expression matrix of pulpitis, aiming to identify biological pathways and diagnostic biomarkers of pulpitis. (researchsquare.com)
GO analysis revealed that the DEGs were enriched in biological processes related to inflammation, and the enriched pathways in the KEGG pathway analysis were cytokine-cytokine receptor interaction, chemokine signalling pathway and NF-κB signalling pathway. (researchsquare.com)
The initial functional clustering, signaling pathways and protein-protein interaction relationship analyses were conducted using the DAVID and STRING software programs. (minervamedica.it)
BACKGROUND: Gene set analysis (GSA) has become a successful tool to interpret gene expression profiles in terms of biological functions, molecular pathways, or genomic locations. (uky.edu)
Ingenuity Pathway Analysis (IPA) found that several carcinogenic-related signaling pathways and carcinogenesis itself were associated with both the 7 and 11 gene signatures. (cdc.gov)
Two of these genes, arginase 1 and eotaxin 1 are the focus of continuing investigations in mouse models of asthma regarding differences in mechanistic pathways depending on the allergen. (cdc.gov)
Array studies provide candidate genes to identify common mechanistic pathways in the effector phase, as well as mechanistic pathways unique to individual allergens. (cdc.gov)

The reviewer also asked question about gene set enrichment analysis, which I believe is written slightly confusing way. (peerj.com)

In genetics and genomics research, gene expression refers to the process by which information encoded in a gene's DNA sequence is converted into functional proteins or RNA molecules. (pharmiweb.com)
Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics.This typically involves the visualization of a few proteins or expressed genes at a time. (lu.se)
Bortoluzzi S, Alessi FD, Romualdi C, Danieli GA: Differential expression of genes coding for ribosomal proteins in different human tissues. (karger.com)
Protein-protein interaction (PPI) networks and modules were constructed to identify hub genes with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape. (researchsquare.com)
Immunohistochemical staining was performed to confirm the expression of related proteins in OA and non‑OA tissue samples. (spandidos-publications.com)
Genes encoding disrupted complementary interactors tend to be risk genes, and an interaction network built from these proteins is enriched for ASD proteins. (springer.com)

We used a genome-wide analysis which not only examined differential gene expression levels but could also detect differences in splice isoform usage. (jneurosci.org)
Advances in genome -wide analysis of host-pathogen interactions have provided the necessary tools to investigate molecular factors that directly contribute to S. aureus pathogenesis . (bvsalud.org)

The progress being made by a number of companies and academic researchers enabling resolution of questions from genomic analysis was shared at the recent "Plant and Animal Conference" in San Diego. (genengnews.com)
This alignment process enables the determination of the origin of each read, allowing us to associate it with specific genes or genomic regions. (pharmiweb.com)
We investigate the functional relevance of de novo missense variants, specifically whether they are likely to disrupt protein interactions, and nominate novel genes in risk for ASD through integrated genomic, transcriptomic, and proteomic analyses. (springer.com)

Using sequence databases a researcher can usually determine, with some confidence, from which original mRNA (and therefore which gene) the tag was extracted. (wikipedia.org)
In addition, the mRNA sequences do not need to be known a priori, so genes or gene variants which are not known can be discovered. (wikipedia.org)
We provide a searchable web resource for exploring differential mRNA expression and splice form usage between excitatory, PV, SST, and VIP neurons ( http://research-pub.gene.com/NeuronSubtypeTranscriptomes ). (jneurosci.org)
We sorted excitatory neurons and key inhibitory neuron subtypes from mouse brains and assessed differential mRNA expression. (jneurosci.org)
In this study, we examined the expressions of p33ING1, p14ARF, MDM2 and p21WAF1 mRNA in 25 advanced colorectal cancers by quantitative RT-PCR method, and compared the expression levels of p33ING1, p14ARF, p21WAF1 and MDM2 in relation to p53 status in the tumors. (nih.gov)
Interestingly, in eight cases with p53 wild-type gene, 6 cases (75%) showed a marked down-regulation of p14ARF mRNA, and three cases (37.5%) over-expressed MDM2 mRNA. (nih.gov)
In all cases, high levels (with differences among strains) of GPD1 mRNA but quite low expression of other stress genes (TRX2, HSP104 and SSA3) were found. (unboundmedicine.com)
For all these genes, mRNA levels increase as temperature decreases or pH increases. (unboundmedicine.com)
Southern and Northern analyses, using DNA and RNA extracted from infected Cf-124T cells, revealed the presence of both TrV1- and TrV4-carrying genome segments and transcripts, but neither DNA, at least in episomal form, nor mRNA persisted for more than a few days p.i. (gc.ca)
This research project attempts to identify the genetic determinants of SHRSP/Gla phenotypes by using mRNA and micro(mi)RNA expression profiling data, in combination with the genome sequence of the SHRSP/Gla and WKY/Gla, to facilitate human translational studies for hypertension and vice versa. (gla.ac.uk)
Furthermore, 4 genes from these two sets of significant genes, coiled-coil domain containing-99 (Ccdc99), muscle segment homeobox gene-2 (Msx2), nitric oxide synthase-2 (Nos2), and wingless-type inhibitory factor-1 (Wif1), showed significant mRNA expression perturbations at both time points. (cdc.gov)

This resource, combining a unique new dataset and novel application of analysis methods to multiple relevant datasets, identifies numerous potential drug targets for manipulating circuit function, reveals neuron subtype-specific roles for disease-linked genes, and is useful for understanding gene expression changes observed in human patient brains. (jneurosci.org)
We also apply our analysis to two other relevant datasets for comparison, and provide a searchable website for convenient access to the resource. (jneurosci.org)
In this study, the experimental design involved splitting the gene profiles into training and testing datasets, randomly selecting groups of profiles, determining the modeling parameters of the genes to postmortem time using over- and/or perfectly- defined linear regression analyses, and calculating the fit (R 2 ) and slope of predicted versus actual postmortem times. (biorxiv.org)
This paper analyzes gene expression datasets from cervical cancer microarray data. (peerj.com)

Using a lentiviral vector containing either H-Ras oncogene and a hairpin targeting p53 or both tumor suppressor genes, NF-1 and p53, Dr. Friedmann-Morvinski can induce the formation of a glioma tumor in mice injected in the brain. (genengnews.com)

For example, a normal tissue sample can be compared against a corresponding tumor to determine which genes tend to be more (or less) active. (wikipedia.org)
With RNA-seq , we can capture and quantify the abundance of transcripts, revealing the dynamic landscape of gene expression within a cell or tissue. (pharmiweb.com)
By comparing gene expression patterns during embryogenesis or tissue differentiation, we unravel the molecular events that shape organisms, advancing our understanding of developmental biology. (pharmiweb.com)
We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. (lu.se)
Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics. (lu.se)
Activation of tissue-specific gene expression of the components of the renin-angiotensin system (RAS) in humans may play an important role in cardiovascular regulation and pathophysiology. (jci.org)
Studies of human tissue RAS expression, however, have been limited by the lack of availability of sufficient amounts of fresh human tissues and a sensitive method for detecting specific mRNAs. (jci.org)
In order to study changes of gene expression in small tissue samples (e.g., renal biopsies) obtained from patients, we established a competitive PCR assay for quantification of renin, using a 155-basepair deletion mutant of the human renin cDNA as an internal standard. (jci.org)
A total of 470 DEGs comprising 394 upregulated and 76 downregulated genes were found in pulpitis tissue. (researchsquare.com)
Four stanniocalcin genes in teleost fish: structure, phylogenetic analysis, tissue distribution and expression during hypercalcemic challenge. (ualg.pt)
The test is based on the combined analysis of 12 genes in formalin-fixed, paraffin-embedded (FFPE) tissue by reverse transcription-quantitative real-time PCR (RT-qPCR). (biomedcentral.com)
Gene expression values to calculate the EP score were assayed by one-step RT-qPCR using RNA from FFPE tumor tissue. (biomedcentral.com)
Using the newly released and larger ASC dataset, we confirm these observations and take them in several new directions: (1) By defining a set of genes encoding these disrupted protein interactors in ASD subjects and another for their siblings, we evaluate their expression patterns in developing brain from fetal to early postnatal development and within general cell types of brain tissue. (springer.com)

Ten DEGs, including 7 hub genes from PPI analysis, were confirmed by real-time PCR. (medscimonit.com)

CONCLUSIONS: Important levels of expression of GPD1 (but not of other stress genes) are required during the first hours of vinification, because of the need for glycerol production to counteract the hyperosmotic stress at this point. (unboundmedicine.com)
CONCLUSIONS: We found that ICAM1 and other genes may play a role in the development of disc degeneration induced by inflammatory reactions using a bioinformatics analysis of the gene expression profiles of degenerative intervertebral disc cells stimulated with inflammatory factors, suggesting that bioinformatics methods can be used to identify potential target for intervertebral disc degeneration. (minervamedica.it)
CONCLUSIONS: The simulation study and the real data application showed that the proposed gene set analysis provides a promising tool for longitudinal microarray analysis. (uky.edu)

Statistical methods are employed to identify genes that exhibit significant changes in expression between experimental conditions. (pharmiweb.com)

Functional annotation clustering of the microarray data showed that gene clusters involved in immune and antiviral responses ranked highly, involving genes such as chemokine (C-C motif) ligand 2 ( CCL2 ), chemokine (C-C motif) ligand 5 ( CCL5 ), chemokine (C-X-C motif) ligand 10 ( CXCL10 ), and toll like receptor 3 ( TLR3 ). (molvis.org)
BACKGROUND: To investigate the microarray data on the gene expression profiles of intervertebral disc degeneration related to cytokine exposure. (minervamedica.it)
Raw microarray data is available in Gene Expression Omnibus (National Center for Biotechnology Information) with accession number GSE6085. (uky.edu)

In today's research laboratory, two common ways that gene expression is assessed is by using quantitative polymerase chain reaction techniques (QTPCR) for monitoring expression of smaller numbers of genes, and by employing DNA microarrays for the highly parallel monitoring of thousands of genes (or the whole transcriptome). (ddw-online.com)
Gene expression signature of human neuropathic pain identified through transcriptome analysis. (iasp-pain.org)
This study aimed to identify genes associated with neuropathic pain through transcriptome analysis in order to gain a better understanding of the mechanisms underlying this chronic, difficult-to-treat pain. (iasp-pain.org)
We conducted transcriptome analysis using a training datasetof 202 individuals, including patients with neuropathic pain and healthy controls. (iasp-pain.org)
Methodology/Principal Findings: We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. (uni-wuerzburg.de)
A combination of de novo transcriptome assembly and DGE analysis was shown to be a powerful method for identifying genes encoding enzymes potentially involved in the biosynthesis of important secondary metabolites in a non-model plant. (biomedcentral.com)
Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. (nature.com)

Scientists armed with whole genome sequence data can now ask questions about genome structure and organization that impact gene expression. (genengnews.com)
Analysis of gene expression can include measuring expression levels of a small set of genes to whole genome expression monitoring. (ddw-online.com)
In terms of the distribution of identified genes in a specific category relative to the whole genome, only the categories of PE/PPE and conserved hypotheticals have statistical significance. (hindawi.com)

Improved access to bioinformatics tools enables scientists to process, manage, and store raw data, annotate sequences to define genes, and quantitate RNA sequence data to get insight into gene expression patterns. (genengnews.com)
Previous data has reported similarity between human brain and testis gene expression patterns. (karger.com)
Hence, it means that human testis could also play a crucial role in human speciation if these two tissues exhibit similar gene expression patterns. (karger.com)
Determining the large scale anatomy of gene expression patterns of various human tissues could draw a more convincing conclusion, and better our understanding of the correlation/inter-correlation among different tissues. (karger.com)
Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. (karger.com)
Present results provide evidence to support the proposal that human testis and brain share the highest similarity of gene expression patterns. (karger.com)
Accordingly, an important extension of our work on evolutionary patterns of human genetic diseases would be to incorporate gene expression as another level of analysis. (irb.hr)
For genes encoding the disrupted interactions, we evaluate their expression patterns across developing brains and within specific cell types, using both bulk and inferred cell-type-specific brain transcriptomes. (springer.com)
This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. (biomedcentral.com)

Quantitative analysis by the polymerase chain reaction. (jci.org)
Quantitative real-time PCR analysis of 23 genes was used to validate the microarray results. (molvis.org)
We analyse by means of quantitative PCR the expression of several stress induced genes in 24 efficient commercial wine yeast strains at the beginning of vinifications performed under standard conditions or with small variations in pH and temperature. (unboundmedicine.com)
Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. (nature.com)
This relationship was further verified through a quantitative PCR analysis where we demonstrated a significant correlation between the expression of these prefrontal dopamine genes and the general learning abilities of 48 mice. (rutgers.edu)
A total of 63 identified lung cancer prognostic biomarker genes and major signaling biomarker genes were analyzed in mouse lungs (n=80) exposed to 0, 10, 20, 40, or 80µg of MWCNT by pharyngeal aspiration at 7 and 56days post-exposure using quantitative PCR assays. (cdc.gov)

We constructed a neuropathic pain signature using these five genes and validated it using an independent dataset of 25 individuals. (iasp-pain.org)
We plan to generate a genome-wide microarray expression dataset which covers full ontogeny of zebrafish in high resolution. (irb.hr)

Statistical methods can be applied to tag and count lists from different samples in order to determine which genes are more highly expressed. (wikipedia.org)
After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. (frontiersin.org)
From the beginning, the main issues related to such DE analysis have been pointed out, and many methods and tools have been proposed in the relevant literature. (frontiersin.org)
Here, we introduce these issues and review some widely used methods and tools for DE analysis. (frontiersin.org)
This review will help us to choose the most relevant methods and tools to perform DE analyses in the present work. (frontiersin.org)
In this review, we summarize the basic theories and analysis methods about codon bias, and introduce the application of codon bias analysis in foreign gene expression in three categories of fungi - yeasts, molds and mushrooms respectively. (novapublishers.com)
This chapter describes methods to analyze gene expression in S. aureus during interaction with human neutrophils . (bvsalud.org)
Different statistical methods with varying selection criteria resulted in identification of similar candidate genes. (cdc.gov)

It is generally hypothesized to be related to aging, trauma, inflammation, obesity, metabolism and genetics, and may also be related to genetic factors, chromosomal abnormalities and gene fusion ( 5 , 6 ). (spandidos-publications.com)
Both genetics and environmental factors influence the expression of asthma, and not all asthma is the result of a specific immune response to allergen. (cdc.gov)

Differential Gene Expression analysis is a fundamental tool for identifying genes whose expression levels significantly differ between experimental conditions or biological samples. (pharmiweb.com)
A total of 74,179 microarray probes were calibrated using the Gene Meter approach and the transcriptional profiles of 1,063 significantly upregulated genes were assembled into a time series spanning from life to 48 or 96 h postmortem. (biorxiv.org)
The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. (frontiersin.org)
In contrast, culturing on Laminin-421 induced the expression of β-cell genes, including Ins1 , MafA , and Glut2 , and significantly improved glucose-stimulated insulin secretion. (nature.com)
This method was used for an IL-2 stimulation study and significantly altered gene sets were identified. (uky.edu)

In recent years, our understanding of genetic predisposition to PD has advanced vastly, including causative mutations in the genes encoding α-synuclein, LRRK2, parkin, PINK1, and DJ-1 just to name a few 5 . (nature.com)
Mutations of p53 tumor suppressor gene increase with tumor progression in colorectal cancers. (nih.gov)
A classic example is the heat shock protein system, particularly Hsp90 , whose expression is environmentally plastic and increases under thermal stress, but buffers phenotypic changes induced by mutations to maintain homeostasis 2 , a process termed canalization 3 . (nature.com)
PCR-sequencing and qRT-PCR were performed to compare mutations and expression levels of MTases in different strains. (ac.ir)
Only two mutations were found in isoniazid resistance (INH R ) strain for Rv3919c (T to G in codon 341) and Rv1392 (G to A in codon 97) genes. (ac.ir)
Mutations in the AMER1 gene have been found in Wilms tumor, a rare form of kidney cancer that occurs almost exclusively in children. (medlineplus.gov)
AMER1 gene mutations result in a protein with a reduced ability to repress Wnt signaling. (medlineplus.gov)
Mutations in the AMER1 gene that are present in cells throughout the body (called germline mutations) cause a bone disorder called osteopathia striata with cranial sclerosis. (medlineplus.gov)
AMER1 gene mutations that cause osteopathia striata with cranial sclerosis lead to a lack of functional AMER1 protein, disrupting its role in regulating the Wnt signaling pathway. (medlineplus.gov)

These annotations are used as experimental factors and the user can analyze differences in gene expression between the annotation type values. (lu.se)

By analyzing the expression levels of thousands of genes simultaneously, researchers can identify genes that are upregulated (higher expression) or downregulated (lower expression) in one condition compared to another. (pharmiweb.com)

Amy Radunz, a nutritionist from the department of animal sciences at the University of Wisconsin in River Falls, has partnered with molecular biologist Hasan Khatib, an associate professor at University of Wisconsin-Madison, to ask how differences in maternal diet during pregnancy induce gene expression and DNA methylation changes in fetal tissues in sheep. (genengnews.com)
The study also looked at the impact of paternally expressed genes: IGF2, PEG1, PEG3, DLK1, and DIO3 for transcriptomic and epigenomic alterations of the imprinted genes in fetal tissues. (genengnews.com)
When studying gene expression, researchers often compare gene expression profiles between different biological samples or experimental conditions, such as healthy and diseased tissues, treated and untreated cells, or different developmental stages. (pharmiweb.com)
Usage information: Gene expression of the renin-angiotensin system in human tissues. (jci.org)
Gene expression of the renin-angiotensin system in human tissues. (jci.org)
The AMER1 gene provides instructions for making a protein found in tissues throughout the body where it helps regulate the Wnt signaling pathway, which is a series of chemical signals that affect the way cells and tissues develop. (medlineplus.gov)

Array data are intended to provide candidate genes for hypothesis generation and further experimentation. (cdc.gov)

Aim: To detect the expression of molecules associated with Notch signaling pathway in stem cells from human exfoliated deciduous teeth (SHED) cultured in specific differentiation medium, namely, keratinocyte growth medium (KGM). (bvsalud.org)

Taking advantage of Qlucore Omics Explorer's powerful data analysis capabilities, its speed, and its ability to work on any PC, Dr Bárbara Meléndez and her colleagues in the Unidad de Investigación de Patología Molecular (Molecular Pathology Research Unit) at Hospital Virgen de la Salud in Toledo, Spain, are investigating how such generally benign meningiomas can start to exhibit the sort of histology and recurrence usually associated with more aggressive tumours. (scientistlive.com)
In order to do this, Meléndez and her team are using Qlucore Omics Explorer to perform gene expression and methylation analyses of brain tumour samples and then validating them with data from other databases. (scientistlive.com)
Each sample can generate around 41,000 gene expression data, resulting in huge data files because of the number of samples involved (Fig. 1). (scientistlive.com)
Supervised analyses have allowed us to identify gene expression profiles associated with more aggressive tumours - findings that have been confirmed by analysing the methylation data with Qlucore,' she concludes. (scientistlive.com)
As for any other statistical analysis, one main issue has been finding the probabilistic model that best fits the data, as well as the optimal parameter estimates of this model. (frontiersin.org)
and (4) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry. (lu.se)
A Comparative Analysis of Gene-Expression Data of Multiple Cancer Typ" by Kun Xu, Juan Cui et al. (unl.edu)
Indeed, by applying phylostratigraphy on human genome data we were able to show that evolutionary origin of disease genes is not random. (irb.hr)
Finally, we integrate protein interactions and cell-type-specific co-expression networks together with published association data to implicate novel genes in ASD risk in a cell-type-specific manner. (springer.com)
An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (biomedcentral.com)
Gene set analysis for longitudinal gene expression data" by Ke Zhang, Haiyan Wang et al. (uky.edu)
11), altered liver structure and function (12), altered naire data from 8,765 children aged 5 to 7 years, smoking gene expression (13), and possibly type 2 diabetes mel- after pregnancy was not associated with childhood obesity litus (10). (cdc.gov)
Micro- array data from the ovalbumin and TMA model of asthma were also compared to previous data using Aspergillus as allergen to identify putative asthma `signature genes', i.e. genes up-regulated with all 3 allergens. (cdc.gov)

Serial Analysis of Gene Expression (SAGE) is a transcriptomic technique used by molecular biologists to produce a snapshot of the messenger RNA population in a sample of interest in the form of small tags that correspond to fragments of those transcripts. (wikipedia.org)

This method was used to measure the number of copies of repeated genes such as rRNA genes (2) and to measure whether specific genes were under-replicated during the replication process used in forming polytene chromosomes (3). (ddw-online.com)

This design was repeated several thousand to million times to find the top predictive groups of gene transcription profiles. (biorxiv.org)
We used the paradigmatic GATA-PU.1 axis to explore, at the systems level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. (lu.se)
Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division. (karger.com)
These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. (frontiersin.org)
Rearrangements may also indirectly affect global gene expression if homoeologous copies of gene regulators within rearrangements have differential affects on the transcription of genes in networks. (purdue.edu)

To clarify the biological rationale for social regulation of gene expression, this study sought to identify the specific immune cell types that are transcriptionally sensitive to subjective social isolation (loneliness). (nih.gov)
While the main drawback of previous relevant studies is the lack of generality, we conducted both an analysis of a two-condition experiment (with eight biological replicates per condition) to compare the results with previous benchmark studies, and a meta-analysis of 17 experiments with up to 18 biological conditions, eight biological replicates and 100 million (M) reads per sample. (frontiersin.org)
For individuals working on tomato research, on the basis of the meta-analysis, we recommend at least four biological replicates per condition and 20 M reads per sample to be almost sure of obtaining about 1000 DE genes if they exist. (frontiersin.org)
Nowadays, an increasing number of microarray studies are conducted to explore the dynamic changes of gene expression in a variety of species and biological scenarios. (uky.edu)
1998. Blood and breath analyses as biological indicators of exposure to trihalomethanes in indoor swimming pools. (cdc.gov)

Audic S, Claverie JM: The significance of digital gene expression profiles. (karger.com)

Together, our work revealed how PARIS drives adverse effects on modulation of PPAR-γ associated gene clusters in DA neurons. (nature.com)
A total of 25 important modules were generated, and two core gene clusters and seven core genes were obtained (COL6A2, COL5A2, COL12A1, COL5A1, COL6A1, LUM and COL3A1). (spandidos-publications.com)
The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. (uni-wuerzburg.de)

The title of the abstract is "A Randomized Phase II Study of Co-Expression Extrapolation (COXEN) with Neoadjuvant Chemotherapy for Localized, Muscle-Invasive Bladder Cancer. (bioquicknews.com)

Seven putative mycobacterial MTase genes ( Rv0645c , Rv2966c , Rv1988 , Rv1694 , Rv3919c , Rv2756c , and Rv3263 ) and Rv1392 as SAM synthase were selected for analysis. (ac.ir)

Two of the most common uses of the DNA microarrays are genetic analysis and the analysis of gene expression. (ddw-online.com)
This report will focus in using DNA microarrays for the analysis of gene expression or expression profiling, and how DNA chips are used for drug discovery and development. (ddw-online.com)
We utilized Arabidopsis 70mer oligonucleotide microarrays for exploring gene expression in three resynthesized B. napus lineages at the S0:1 and S5:6 generations as well as their diploid progenitors B. rapa and B. oleracea . (purdue.edu)

Once the reads are mapped, we quantify the expression level of each gene. (pharmiweb.com)
The method described here may serve as a highly sensitive tool to quantify alterations in gene expression in man under various pathophysiologic conditions. (jci.org)
In the present set of experiments, using gene-expression microarray technology that allowed us to quantify the expression of ~25,000 genes simultaneously, we assessed the gene expression profiles of the best and worst learners from a sample of 60 mice (in two replications). (rutgers.edu)

This analysis enables us to pinpoint genes that play pivotal roles in phenotypic variation, disease development, or response to treatments. (pharmiweb.com)
DGE analysis facilitates the identification of genes responsive to specific drug treatments. (pharmiweb.com)
RESULTS: We provide a robust nonparametric approach to compare the expressions of longitudinally measured sets of genes under multiple treatments or experimental conditions. (uky.edu)

Weighted gene co‑expression network analysis was performed, and a protein‑protein interaction network was constructed and further analyzed using Cytoscape and STRING. (spandidos-publications.com)
The interaction network analysis indicated that PTGS2, ICAM1, NOV and other genes may play a role in disc degeneration. (minervamedica.it)
Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks are highly conserved across environments. (nature.com)

The significance of this study is two-fold: selected groups of upregulated genes provide accurate prediction of postmortem time, and the successfully validated experimental design can now be used to accurately predict postmortem time in cadavers. (biorxiv.org)
This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement. (frontiersin.org)
This study provides a differential gene expression profile between TMJ fibrous and bony ankylosis. (medscimonit.com)
Further study of these key genes may provide new ideas for future treatment of TMJ bony ankylosis. (medscimonit.com)
This in vitro system may provide a suitable starting point for the study of TrIV gene functions. (gc.ca)
Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. (uni-wuerzburg.de)
Our study has identified 42 genes specifically induced by capreomycin and PA-824. (hindawi.com)
Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. (hindawi.com)
In the present study, the effect of MSG on cell viability and its effect on expression of APC , BECN1 , and TP53 genes in SW620 and SW480 colon cancer cell lines were studied. (scielo.br)

Currently, researchers have encountered low expression level in many fungi transgenic research, so it is of great practical significance and economical value to investigate the application of codon bias analysis in foreign gene expression in fungi. (novapublishers.com)

Advances in genomics technology have made sequence analysis of diverse organisms routine. (genengnews.com)
W. B. Wang, S. Y. Zhu, L. Q. Wang, F. Yu, Shen W. D. (2005) Cloning and sequence analysis of the Antheraea pernyi nucleo-polyhedrovirus gp64 gene. (scirp.org)
S. Gomi, K. Majima, Maeda S. (1999) Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. (scirp.org)
E. A. van Strien, D. Zuidema, R.W. Goldbach, Vlak, J. M. (1992) Nucleotide sequence and transcriptional analysis of the polyhedrin gene of Spodoptera exigua nuclear polyhedrosis vi-rus. (scirp.org)
The sequence analysis of the 32-35,000 predicted genes indicates the there may be as many as 1,000 kinase or kinase-like genes. (ddw-online.com)
in fact, the non-coding regions of all three genes show higher sequence identity than the coding regions, pointing to their common origin. (gc.ca)

The polyhedrin (polh) gene is often used to analyse evolution of baculovirus. (scirp.org)
In addition, oligonucleotide probes are used to analyse gene expression. (scientistlive.com)

Here, we sought to validate an experimental design to accurately predict the time of death by analyzing the expression of hundreds of upregulated genes in two model organisms, the zebrafish and mouse. (biorxiv.org)
The correspondence, heat map, and dendrogram analyses independently suggest a differential, Background: Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions. (uni-wuerzburg.de)

Stanniocalcin (STC), first isolated from the corpuscles of Stannius (CS) of teleost fishes and a systemic regulator of mineral metabolism, is present in all vertebrates as two isoforms, STC1 and STC2, encoded by separate genes. (ualg.pt)

To understand the molecular-genetic basis of functional specialization and identify potential drug targets specific to each neuron subtype, we performed a genome wide assessment of both gene expression and splicing across EXC, PV, SST and VIP neurons from male and female mouse brains. (jneurosci.org)
These results reveal numerous examples where neuron subtype-specific gene expression, as well as splice-isoform usage, can explain functional differences between neuron subtypes, including in presynaptic plasticity, postsynaptic receptor function, and synaptic connectivity specification. (jneurosci.org)
This analysis reveals numerous examples of neuron subtype-specific isoform usage with functional importance, identifies potential drug targets, and provides insight into the neuron subtypes involved in psychiatric disease. (jneurosci.org)
Tools like the TIGR Gene index [ 35 ] and Unigene [ 36 ] provide significant information on many species, yet these databases do not meet the needs of functional genomics projects for many non-model species. (biomedcentral.com)

L. H. Robert, Bonning B.C. (2003) Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedroviruses Journal of General Virology 84, 1827-1842. (scirp.org)
In conclusion, both stc1 and stc2 genes are represented by paralogues in teleosts genomes and the analysis performed suggests that only stc1-a in the CS is involved in extracellular calcium regulation. (ualg.pt)

A group of eleven zebrafish genes yielded R 2 of 1 and a slope of 0.99, while a group of seven mouse liver genes yielded a R 2 of 0.98 and a slope of 0.97, and seven mouse brain genes yielded a R 2 of 0.93 and a slope of 0.85. (biorxiv.org)

Bertelsen A.H., Velculescu V.E., High-throughput gene expression analysis using SAGE, Drug Discovery Today 3 (1998) 152-159. (gse-journal.org)
1998. Profiles of Great Lakes critical pollutants: A sentinel analysis of human blood and urine. (cdc.gov)

TP53 is a tumor suppressor gene that functions in modifying DNA errors and/or inducing apoptosis of damaged cells, and both APC and BECN1 genes are involved in CRC and are of importance in cellular growth and metastasis. (scielo.br)

Receiver operating characteristic (ROC) curve analysis demonstrated that this signature had a high level of accuracy in differentiating between neuropathic pain patients and healthy controls, with an area under the curve (AUC) of 0.83 (95% CI 0.65-1). (iasp-pain.org)
These findings suggest that these five genes may be potential therapeutic targets for neuropathic pain. (iasp-pain.org)

Comparative Toxicogenomics Database and TargetScan were used to identify the hub‑gene‑related diseases and the microRNAs that regulated the central hub genes. (spandidos-publications.com)
Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution. (cdc.gov)

RNA extracted from mock-infected and WNV-infected cells was assessed for differential expression of genes using Affymetrix microarray. (molvis.org)

Using Qlucore principal component analysis (PCA) the team can identify groups of tumours that have the same histopathology, despite being different at the molecular level. (scientistlive.com)
Examples of high molecular environmental factors are known to influence the development weight occupational allergens include proteases used in the and expression of asthma, and a vast array of triggers of asthma detergent industry, laboratory animal allergens, and ovalbumin have been identified. (cdc.gov)

The nCounter® Analysis System provides a cost-effective automated solution for multiplex expression analysis of 800+ targets. (nanostring.com)
The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)

This is a unique feature and a technical advance in comparison with existing RNA-based prognostic multigene expression tests. (biomedcentral.com)

Evolutionarily ancient myeloid antigen-presenting cells appear to have evolved a transcriptional sensitivity to socioenvironmental conditions that may allow them to shift basal gene expression profiles to counter the changing microbial threats associated with hostile vs. affine social conditions. (nih.gov)
Anonymous Reviewer ( 2018 ) Peer Review #2 of 'Integrative machine learning analysis of multiple gene expression profiles in cervical cancer (v0.3)' . (peerj.com)
Wong K ( 2018 ) Peer Review #1 of 'Integrative machine learning analysis of multiple gene expression profiles in cervical cancer (v0.2)' . (peerj.com)

Expression analyses allowed us to identify that meningiomas can be classified into an aggressive and a non-aggressive group - despite WHO classification criteria establishing three malignancy groups and about 15 histopathological subtypes. (scientistlive.com)
Disrupted protein interactions identify gene sets involved in risk for ASD. (springer.com)
Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis. (cdc.gov)

Dr. Thoedorescu's lab used 60 human-derived cancer cell lines curated by the National Cancer Institute to develop a gene expression approach to predicting the sensitivity of these cells to various chemotherapies. (bioquicknews.com)

Anatomy26

Organisms16

Diseases4

Chemicals and Drugs70

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes101

Disciplines and Occupations4

Information Science8

Health Care3

Differentially20

Ontology7

Pathways8

Enrichment analysis1

Proteins6

Genome-wide analysis2

Genomic3

MRNA11

Datasets4

Tumor suppr1

Tissue13

DEGs1

Conclusions3

Employed to identify genes1

Microarray data3

Transcriptome7

Whole genome3

Patterns9

Quantitative6

Dataset2

Methods8

Genetics2

Significantly5

Mutations9

Annotation1

Thousands of genes1

Tissues6

Candidate Genes1

Pathway1

Data13

Transcriptomic1

Specific genes1

Transcription5

Biological5

Digital gene expression1

Clusters3

Abstract1

Putative1

Microarrays3

Quantify3

Treatments3

Interaction3

Study9

Significance1

Sequence6

Analyse2

Experimental2

Teleost1

Functional4

Genomes2

Zebrafish1

19982

Apoptosis1

Neuropathic2

Comparative2

Affymetrix1

Molecular2

Targets2

Prognostic1

Profiles3

Identify3

Human1