Identification of differentially expressed genes gene expression. Medical search. Frequent questions

For this reason, we performed differential expression analysis on different expression profiles of COVID-19 patients, using RNA-Seq data coming from NCBI public repository, and we obtained the lists of all differentially expressed genes (DEGs) emerging from 7 experimental conditions. (unict.it)
We performed a Gene Set Enrichment Analysis (GSEA) on these genes to find possible correlations between DEGs and known disease phenotypes. (unict.it)
We mainly focused on DEGs coming out from the analysis of the contrasts involving severe conditions to infer any possible relation between a worsening of the clinical picture and an over-representation of specific genes. (unict.it)
RNA-seq offers several advantages over microarrays or RT-qPCR for detecting differentially expressed genes (DEGs). (biomedcentral.com)
We explored the differentially expressed genes (DEGs) in the dataset and conducted Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the potential hub genes. (iasp-pain.org)
Differentially expressed genes (DEGs) were identified by comparing the gene expression of NIDCM patients with or without VA in the gene expression profile of GSE135055. (hindawi.com)
A total of 228 DEGs were obtained, and 3 genes were screened out to be significantly related to the survival time of NIDCM patients. (hindawi.com)
In order to reveal the inherent molecular mechanism, NIDCM patients were divided into sinus rhythm (SR) group and VA group and differentially expressed genes (DEGs) were identified via bioinformatic methods. (hindawi.com)
Moreover, RNA-seq results indicated that 46 differentially expressed genes (DEGs) involved in meiotic cell cycle, synaptonemal complex assembly and spermatogenesis were upregulated in the hemicastration group, while 197 DEGs were downregulated, which were related to arachidonic acid metabolism. (animbiosci.org)
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)
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)
Identification of DEGs between healthy and diseased tissues unveils potential diagnostic or prognostic biomarkers. (pharmiweb.com)
The differentially expressed genes (DEGs) were screened by the 'limma' package and hub modules were identified by weighted gene co-expression network analysis (WGCNA). (biomedcentral.com)
Subsequently, gene function annotations were performed to investigate the biological role of the genes from the intersection of two groups (hub module and DEGs). (biomedcentral.com)
In this study, transcriptomic analysis was performed for muscle tissue of G. haimaensis in the in situ environment (MH) and laboratory environment for 0 h (M0), 3 h (M3) and 9 h (M9), and 187,368 transcript sequences and 22,924 annotated differentially expressed genes (DEGs) were generated. (biomedcentral.com)
Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DEGs were enriched with a broad spectrum of biological processes and pathways, including those associated with antioxidants, apoptosis, chaperones, immunity and metabolism. (biomedcentral.com)
Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed genes (DEGs). (spandidos-publications.com)
Moreover, expression levels of DEGs were verified in HNSCC cells and tissues using reverse transcription‑quantitative (RT‑q)PCR. (spandidos-publications.com)
Thus, based on the differentially expressed genes (DEGs) of mitophagy-related tumor classification, we established a 13-gene signature and robust nomogram for predicting BC prognosis, which can be beneficial for the diagnosis and treatment of BC. (aging-us.com)
In our analysis, we established a stable signature, including 13 genes, based on differentially expressed genes (DEGs) in mitophagy-related tumor classification. (aging-us.com)
Our network-based approach aided in the identification of co-expression modules enriched in differentially expressing genes (DEGs) during different stages of COVID-19 and enabled discovery of novel genes involved in the COVID-19 pathogenesis, by virtue of their transcript abundance and association with genes expressing differentially in modules enriched in DEGs. (cdc.gov)

Five of the 6 most significant gene ontology pathways involve inflammation and activation of the immune response with CD28 and CTLA signaling of Tcells. (scienceblog.com)
Gene ontology (GO) analysis revealed that inflammatory pathways were most frequently implicated in RTK. (aging-us.com)
Whole genome analysis of lung, sampled 24 hours after challenge, showed expression changes of not only genes belonging to several Gene Ontology groups with up-regulation of inflammatory-associated genes and those associated with lung remodeling but also genes involved in downsizing these processes. (cdc.gov)
Bioinformatic analysis of the proteomes revealed shared Gene Ontology (GO) terms and signaling pathways within the clusters of co-expressed proteins (Tables 1-3 and S4. (lu.se)

Microarray analysis of mRNA expression revealed 3034 genes-in-play differentially expressed in C. albicans stomatitis. (scienceblog.com)
Differentially expressed genes were identified via microarray analysis. (cdc.gov)
Here, we examined the expression of the HE4 gene and protein in a large series of normal and malignant adult tissues by oligonucleotide microarray and tissue microarray, respectively. (nature.com)
We download the microarray expression dataset (GSE135055) from the Gene Expression Omnibus (GEO) database [ 9 ]. (hindawi.com)
I propose to study caste-specific gene expression in the fire ant, Solenopsis invicta, with a large ( and gt;20,000 clones) spotted cDNA microarray that was recently developed, sequenced, and annotated at the prospective host institute, the group of Prof. L. Keller at the University of Lausanne. (europa.eu)
To investigate this hypothesis, they perform gene expression analysis using state-of-the-art techniques such as RNA-sequencing or microarray technologies. (heartofamericanorthwest.org)
Statistical tests have been developed for microarray data to identify genes that are differentially expressed relative to a fold change threshold. (biomedcentral.com)
But a microarray comparative experiment is faced with simultaneously assessing a large number of genes based on a small number of biological or technical replicates. (biomedcentral.com)
We will also analyse data from microarray platforms such as gene expression arrays. (lu.se)
The introduction of complementary DNA (cDNA) microarray technology in 1995 has helped to facilitate the identification and classification of DNA sequence information and the assignment of functions to these new genes by allowing investigators to analyze expression of thousands of genes simultaneously in a single experiment. (medscape.com)
[ 5 ] Because a microarray can be used to examine the expression of hundreds or thousands of genes at once, it promises to revolutionize the way gene expression is examined. (medscape.com)
This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. (medscape.com)

In the past decade, microarrays and RT-qPCR have been the primary tools for analyzing gene expression changes. (biomedcentral.com)
Using tissue microarrays and full tissue sections of normal and 448 neoplastic tissues, HE4 immunoreactivity was found in normal glandular epithelium of the female genital tract and breast, the epididymis and vas deferens, respiratory epithelium, distal renal tubules, colonic mucosa, and salivary glands, consistent with HE4 gene expression. (nature.com)
Here, we used oligonucleotide and tissue microarrays to survey HE4 gene and protein expression in a large group of malignant and normal tissues from adults. (nature.com)
18 With the exception of the ovarian neoplasms, the same carcinomas analyzed for gene expression were also examined for HE4 by immunohistochemistry on tissue microarrays (see below). (nature.com)
Because of the recent development of new methods (especially microarrays) for identifying differentially expressed genes, a burst of research on caste differentiation is predicted. (europa.eu)
Gene expression profiles from 128 adult patients with newly diagnosed ALL were characterized using high-density oligonucleotide microarrays. (aacrjournals.org)
Multiplex gene expression studies that are based on microarrays and next-generation sequencing result in the generation of large datasets. (biomedcentral.com)
6. Gene expression analysis by cDNA microarrays / Spyro Mousses, Michael L. Bittner and Yidong Chen / [et al. (edu.au)
A second group of methods, which includes DNA microarrays and proteomics, have advantages that overcome the limitations implicit in signature-tagged mutagenesis and in vivo expression technology, namely, the ability to directly measure expression (gene or protein) levels on a true genome-wide scale, but their application to analysis of bacterial pathogens during real infections is still in its infancy. (cdc.gov)
Microarrays are a significant advance because of their small size and are therefore useful when one wants to survey a large number of genes quickly or when the study sample is small. (medscape.com)
Microarrays may be used to assay gene expression within a single sample or to compare gene expression in 2 different cell types or tissue samples, such as in healthy versus diseased tissue. (medscape.com)
DNA microarrays are simply platforms that consist of small solid supports onto which the sequences from thousands of different genes are attached at fixed locations. (medscape.com)

Mechanistically, the CCL20/CCR6 signaling pathway upregulates HIF-1α by stimulating nuclear factor kappa B-driven transactivation of the HIF1A gene. (cancerindex.org)
RNA profiling identified 2283 differentially expressed genes in F7+F3 treatment, among them genes related to the Wnt signaling pathway and apoptosis-related genes. (nih.gov)

Further, substantial amount of RNA may be required if a large number of genes need to be tested. (biomedcentral.com)

Gene set enrichment analysis (GSEA) for single hub gene revealed that these genes had a close association with antimicrobial response and neutrophils activity. (flu.org.cn)

EXOSC5, MESD, REXO2, and TRMT2A genes are not differentially expressed or not present in the other conditions, being for that reason, good biomarkers candidates for the severe form of COVID-19 disease. (unict.it)
The goal of the study was to compare whole-transcriptome, mucosal gene expression in Candida albicans (a parasitic fungus that can infect the mouth) associated chronic denture stomatitis to that of healthy oral mucosa and perform proteomic analyses of potential salivary biomarkers. (scienceblog.com)
This work provides insight into the temporal effects and mechanistic pathways involved in acute metal intoxication, leading to the identification of candidate biomarkers. (cdc.gov)
Liu S, Huang Z, Deng X, Zou X, Li H, Mu S, Cao B. Identification of key candidate biomarkers for severe influenza infection by integrated bioinformatical analysis and initial clinical validation . (flu.org.cn)
Further validation showed that five of ten hub genes were good prognostic biomarkers for melanoma in two independent groups from the Gene Expression Omnibus database. (jcancer.org)
3. Translational research - to identify predictive biomarkers for treatment decision - by immunohistochemistry, gene expression or sequencing. (lu.se)

This work aims, using RNA sequencing (RNA-Seq) data, to evaluate whether the expression of specific human genes in the host can vary in different grades of disease severity and to determine the molecular origins of the differences in response to SARS-CoV-2 infection in different patients. (unict.it)
Prediction of the coding sequences of unidentified human genes. (wikipedia.org)
HE4 is one of more than 8900 different human genes represented on U95a GeneChips (Affymetrix, Santa Clara, CA, USA), which we used previously to develop a molecular classification of 175 human carcinomas based on patterns of gene expression. (nature.com)

Six extracellular protein genes up-regulated in stomatitis were confirmed within the saliva using proteomic methods. (scienceblog.com)
Dixin is a protein that in humans is encoded by the DIXDC1 gene. (wikipedia.org)
The HE4 (WFDC2) gene encodes a WAP-type four disulphide core domain-containing protein with a presumptive role in natural immunity. (nature.com)
The protein-protein interaction network (PPIN)-based disease candidate gene prioritization uses social and Web networks analysis algorithms (extended versions of the PageRank and HITS algorithms, and the K-Step Markov method). (scienceopen.com)
This gene encodes a member of the beta chemokine receptor family, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. (cancerindex.org)
Alternatively spliced transcript variants that encode the same protein have been described for this gene. (cancerindex.org)
What does this gene/protein do? (cancerindex.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)
Scope includes mutations and abnormal protein expression. (cancerindex.org)
The genome-wide DNA methylation pattern of remaining testis suggested that substantial genes harbored differentially methylated regions (1,139) in gene bodies, which were enriched in process of protein binding and cell adhesion. (animbiosci.org)
Integrative analysis revealed that proteasome 26S subunit ATPase 3 interacting protein gene, which encodes a protein crucial for homologous recombination in spermatocytes, exhibited promoter hypomethylation and higher expression level in hemicastrated mice. (animbiosci.org)
The above genes were calculated in the protein-protein interaction (PPI) network to select the hub genes further. (biomedcentral.com)
The top ten hub genes in immune infiltration-related protein-protein interaction (PPI) networks were selected for further prognostic investigation. (jcancer.org)
Image analysis of the matched maps identified 7 proteins that were either over- or down-expressed: activated protein kinase c receptor (LACK), alpha tubulin (×2), prostaglandin f2-alpha synthase, protein disulfide isomerase, vesicular transport protein and a hypothetical protein. (who.int)
In 2D-DIGE method three protein samples differentially labeled with Cy3-, Cy5- and Cy2-dyes are separated in the same gel. (lu.se)

Methods Onemicroarray dataset was downloaded from the Gene Expression Omnibus (GEO) database. (medicinesci.org)
Here, we examined the expression profile of 108 patients with MDS from the GSE58831 dataset, and identified 22 genes that were significantly associated with overall survival. (frontiersin.org)
Assessing such a large dataset with a small sample size challenges statistical methods: dealing with many genes but few replicates may lead to large Fold Changes (FC) driven by outliers, and to small error variances [ 1 , 2 ]. (biomedcentral.com)
Finally, we added data produced using the 10X genomics system for 7,000 postmitotic progenitors with significantly increased sequencing depth (1,500-11,000 UMI/cell, 1,000-4,000 genes/cell), and observed identical branching patterns as in our original Drop-seq dataset. (authorea.com)
Expression quantitative trait loci (eQTLs) for differentially expressed RNAs were obtained from a publicly available dataset. (lu.se)

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)
Genomic profiling also identifies genes associated with poor outcome in cases without molecular aberrations and specific genes that may be new therapeutic targets in adult ALL. (aacrjournals.org)

MicroRNAs (miRNAs or miRs) are involved in the post-transcriptional regulation of gene expression via complete or partial base pairing with the 3′untranslated region of target genes ( 3 ). (spandidos-publications.com)
SNPs in 6 miRNA processing genes and in 78 miRNAs which target genes known to be important in breast cancer among 906 African American (AA) and 653 European American (EA) cases and Author Manuscript controls enrolled in the Women's Circle of Health Study (WCHS). (cdc.gov)

Obtaining a list of genes which are significantly different between two conditions (e.g. mutant vs wild-type or stimulated vs unstimulated) is central to many transcriptome analyses. (sanger.ac.uk)
Differential Gene Expression analysis is a fundamental tool for identifying genes whose expression levels significantly differ between experimental conditions or biological samples. (pharmiweb.com)
DEX preconditioning significantly improved cardiac dysfunction reduced myocardial infarction size, maintained mitochondrial structural integrity, increased mitochondrial membrane potential, inhibited autophagosomes formation, and decreased ROS production and Beclin1, LC3II/I ratio, PINK1, Parkin, and p62 expression(p (bvsalud.org)
Coincidental with the increased brain Gal-3 in prion-infected animals, the expression of brain trigger receptor expressed in myeloid cell 2 (TREM2), one of the Gal-3 receptors, and some components in the downstream pathway also significantly increased, whereas Toll-like receptor 4 (TLR4), another Gal-3 receptor, and the main components in its downstream signaling were less changed. (bvsalud.org)

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)

MicroRNAs (miRNAs) are small non-coding RNAs that bind complementary messenger RNAs (mRNAs) to repress gene expression and regulate essentially all cellular processes 19 . (nature.com)
We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
Aims/hypothesis: The aim of this study was to identify differentially expressed long non-coding RNAs (lncRNAs) and mRNAs in whole blood of people with type 2 diabetes across five different clusters: severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD), mild obesity-related diabetes (MOD), mild diabetes (MD) and mild diabetes with high HDL-cholesterol (MDH). (lu.se)

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

When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. (biomedcentral.com)
Knowledge of the expression patterns of HE4 in our survey is useful for application in histopathologic diagnosis, and should be taken into consideration in future studies that examine the role of HE4 as a serological tumor biomarker or as a target for gene-based therapy. (nature.com)
Identifying caste-specific patterns of gene expression thus offers a special opportunity to study the generation of adaptive morphological variation by a fundamental biological process, and is the key to profound understanding of the evolution of sociality. (europa.eu)
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)
This is where bioinformatics comes into play - enabling scientists to effectively manage and analyze complex datasets to unravel underlying patterns and potential therapeutic targets related to gene expression changes. (heartofamericanorthwest.org)
tures and gene expression patterns. (lu.se)

This genetic resource will aid in isolating the celastrol biosynthetic genes as well as engineering the celastrol biosynthesis pathway. (techscience.com)

In contrast, Annong1589 showed a passive prevention of the spread of toxins into cells by the upregulation of genes involved in tyramine biosynthesis at the early stage (5 DPA), which may be involved in cell wall strengthening. (biomedcentral.com)
Evidence reported to date suggests overlapping functions for these ligands and their constitutive expression on some normal tissues and upregulation on activated antigen-presenting cells. (thermofisher.com)

FUT6 and CGNL1 were downregulated in HNSCC compared with adjacent healthy tissue and the expression levels of these genes were associated with tumor stage. (spandidos-publications.com)
[ 1 ] the Cancer Genome Anatomy Project index of tumor genes has classified more than 40,000 genes directly or indirectly involved in one or more cancers. (medscape.com)

In this study, we analyzed gene expression of 468 melanoma cases from the TCGA database, which led to the identification of three melanoma clusters (representedby low, median and high infiltration) that display unique immune features. (jcancer.org)
Conclusions/interpretation: Multiple lncRNAs and mRNAs were found to be differentially expressed among clusters and particularly in the MOD cluster. (lu.se)

Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. (scienceopen.com)
The above two groups of genes were intersected to obtain 72 genes for functional annotation analysis. (biomedcentral.com)

Differential expression of miRNAs (DEMs) was identified in bronchial epithelial cells (BECs) isolated from healthy donors and patients with asthma. (medicinesci.org)
Results This study constructed an asthma-associated miRNA-mRNA network, in which seven key miRNAs and 10 hub genes were identified. (medicinesci.org)
A molecular regulatory network consisting of three circRNAs, seven miRNAs and seven mRNAs was constructed, resulting in identification of two signaling axes, hsa_circ_0035431/hsa‑miR‑940/fucosyltransferase 6 (FUT6) and hsa_circ_0035431/hsa‑miR‑940/cingulin‑like 1 (CGNL1). (spandidos-publications.com)
MicroRNAs (miRNAs) are an integral part of the post-transcriptional machinery of gene expression and have been implicated in the carcinogenic cascade. (cdc.gov)
We found a number of SNPs in miRNAs and processing genes in association with breast cancer overall or stratified by estrogen receptor (ER) status. (cdc.gov)

Saliva was analyzed by two-dimensional liquid chromatography and tandem mass spectrometry for proteomic identification of salivary proteins associated with oral Candidiasis. (scienceblog.com)
The identification of a number of immune proteins for therapeutic targeting provides a rationale for investigation into the potential efficacy of earlier intervention with single-agent or combination immunotherapy for ccRCC. (nih.gov)
In particular, BPI and MMP8 encoding proteins in plasma achieved higher expression in severe and dead cases, which indicated an adverse disease development and suggested a frustrating prognosis. (flu.org.cn)
These candidate genes or encoding proteins could be biomarker for clinical diagnosis and therapeutic targets for severe influenza infection. (flu.org.cn)
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)
The expression levels of the mitophagy-associated proteins Beclin1, LC3II/I ratio, p62, PINK1, and Parkin were detected by western blotting. (bvsalud.org)
Multiple gene mutations have been identified and considered as important substrates for the development of MDS, such as RNA splicing, histone manipulation, DNA methylation, transcription factors, kinase signaling, DNA repair, cohesin proteins, and other signal transduction elements. (frontiersin.org)
To reduce the risk of analyzing cell line- pathway can be divided into distinct stages based on the specific features, we used several representative cell lines for recombination status of the Ig genes and on the expression each of four major stages in B cell development: pro-B, pre-B, pattern of surface markers and the presence of intracellular proteins [1- 6]. (lu.se)
Cell proteins were analysed with 2-dimensional electrophoresis and differentially expressed proteins were identified by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. (who.int)
The study shows the usefulness of proteomics in identifying proteins that may express differences between sensitive and resistant L. tropica isolates. (who.int)
Our preliminary study using 2D isolates were recovered from liq- new cases throughout the world cu- gel electrophoresis in drug sensitive/ uid nitrogen, and sub-cultured in taneous leishmaniasis (CL) remains resistant strains of L. tropica showed RPMI1640 medium (Gibco/BRL) a serious public health problem in that some proteins were differentially supplemented with 10% fetal bovine numerous countries [1,2]. (who.int)
At each maturation stage, expression of proteins affects the commitment to move to the next stage. (lu.se)
Defects in genes and proteins important for B cell maturation block the maturation on certain stage and cause primary immunodeficiencies ( IDbase ). (lu.se)

Schematic illustration of the transcriptional bursting model and flowchart of D3E[/caption]We have developed Discrece Distributional Differential Expression (D3E), a method for identifying differentially expressed genes. (sanger.ac.uk)
Therefore, caste differentiation must involve the differential expression of genes that are shared by all castes. (europa.eu)
In preliminary experiments, we have observed that Toxoplasma induce differential expression of over 1000 ISGs, and recombinant IFNg inhibits Toxoplasma, in pig macrophages. (usda.gov)

In conclusion, hsa_circ_0035431 may participate in regulation of FUT6 and CGNL1 expression by sponging hsa‑miR‑940, thus, impacting the occurrence, development and prognosis of HNSCC. (spandidos-publications.com)
However, the efficacy of using pyroptosis-related genes (PRGs) in predicting the prognosis of pancreatic adenocarcinoma (PAAD) patients is unknown. (hindawi.com)
However, the effect of autophagy-related genes (ARGs) on the prognosis of MDS remains unclear. (frontiersin.org)
The median cluster was characterized by an inability to draw immune cells, highlighting possible immune escape mechanisms, and lower CXCL9 and CXCL10 expression, which was correlated to poor prognosis. (jcancer.org)

A P-value of each annotation of a test gene is derived by random sampling of the whole genome. (scienceopen.com)

D3E is specifically designed for single-cell RNA-seq data, and it identifies differentially expressed genes by comparing the full distribution of expression levels for the two conditions rather than just the mean expression. (sanger.ac.uk)

Thus, we conducted a bioinformatics analysis to identify hub genes and key pathways to determine strategies for more effective treatments of CRPS. (iasp-pain.org)

A series of evidence confirm that the five hub genes and the infiltration of seven types of immune cells are related to USML occurrence. (biomedcentral.com)

The advent of synthetic biology opens an alternative avenue to produce celastrol with the prerequisite that genes coding for all the enzymes involved in celastrol biosynthesis are available. (techscience.com)
Transcriptome data were further confirmed by quantitative real-time PCR for twelve key genes in EFA biosynthesis. (researchsquare.com)

The other approach is to screen CRISPR-Cas9-based guide RNA (gRNA) libraries that target either the whole genome using cancer cell and immune cell co-culture systems 9 , 10 , or focused gene sets using immunocompetent murine tumors 11 , 12 . (nature.com)
By converting RNA molecules into complementary DNA (cDNA), followed by fragmentation and library preparation steps, NGS allows for comprehensive profiling of gene expression levels across an entire genome. (heartofamericanorthwest.org)
We have recently applied the NanoString digital platform to study expression of mouse odorant receptor genes, which form with 1,200 members the largest gene family in the mouse genome. (biomedcentral.com)
Although analyses that give information on the expression of a few genes provide insight and have been responsible for a large proportion of the bacterial pathogenesis literature currently available, our ultimate goal is to understand expression changes across the whole genome. (cdc.gov)
The additional information generated by whole genome studies goes far beyond that derived by characterizing in isolation more genes and gene products, because analysis of the whole genome allows complete regulatory networks to be identified and characterized. (cdc.gov)
To contribute to the hazard identification of low molecular weight (LMW) respiratory allergens, respiratory allergy induced by trimellitic anhydride (TMA) was characterized by whole genome analysis of lung tissue and blood proteomics in Brown Norway rats. (cdc.gov)

In this study, we utilized differentially expressed genes screening incorporating weighted gene co-expression network analysis in one eligible influenza GEO data set (GSE111368) to identify hub genes associated with clinical severity. (flu.org.cn)

Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy. (biomedcentral.com)
Results: Eleven lncRNAs and 175 mRNAs were differentially expressed in the MOD cluster, the lncRNA AL354696.2 was upregulated in the SIDD cluster and GPR15 mRNA was downregulated in the MDH cluster. (lu.se)
Because the locations of the probes are known, the intensity and pattern of the labeled mRNA can be used to measure the expression of the targeted gene. (medscape.com)

80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. (mdpi.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)
Gene expression analysis plays a crucial role in understanding the intricate mechanisms underlying biological processes. (heartofamericanorthwest.org)
Gene expression studies often seek to identify genes that are Differentially Expressed (DE) between RNA samples from two types of biological conditions, such as gene knockout mice compared to wild-type mice. (biomedcentral.com)
DE genes can give insights into biological mechanisms or pathways, and form the basis for further experiments. (biomedcentral.com)
The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. (mdpi.com)

These findings provide new insight into severe influenza pathogenesis and identify two significant candidate genes that were superior to the conventional clinical indicators. (flu.org.cn)

A challenge in gene expression studies is the reliable identification of differentially expressed genes. (biomedcentral.com)
The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. (biomedcentral.com)

Osteopontin (OPN) expression was validated by immunohistochemistry. (urotoday.com)

however, the expression in normal and malignant adult tissues has not been examined in detail. (nature.com)
E3 ligase BRUTUS (BTS), a putative iron sensor, is expressed in both root and shoot tissues in seedlings of Arabidopsis thaliana . (molcells.org)
Comparative transcriptome analysis with shoot and root tissues revealed that BTS is involved in regulating energy metabolism by modulating expression of mitochondrial and chloroplast genes in shoot tissues. (molcells.org)
Internal and external validation demonstrated that the five genes were over-expressed in NL tissues compared with USML tissues. (biomedcentral.com)
Central to this investigation is an understanding of what gene products are required and expressed during a natural infection and how this expression changes over time (from initial colonization to causation of disease and spread of the pathogen to new hosts) and space (in different cells or tissues within the host). (cdc.gov)

Our study demonstrates the complexity of FHB resistance in wheat, with cultivars exhibiting unique and overlapping defense mechanisms, and highlights the importance of considering the temporal and spatial dynamics of gene expression in breeding programs for developing more resistant wheat cultivars. (biomedcentral.com)
The model facilitates interpretation of the results, and it makes it possible to generate hypotheses about the underlying mechanisms behind the change in gene expression. (sanger.ac.uk)
Gene expression analysis is a crucial aspect of modern molecular biology research, enabling scientists to gain insights into the intricate mechanisms underlying gene regulation and cellular processes. (heartofamericanorthwest.org)
However, little is known about the genes and mechanisms of resistance acting against M. pinodes in pea. (uni-hannover.de)

Transcriptomic data showed that Sumai3 exhibited a stronger immune response during all stages of grain filling by upregulating genes involved in the active destruction of pathogens and removal of toxins. (biomedcentral.com)
Because the environment encountered within a living host will be quite different from the external environment, pathogens must be able to regulate the necessary genes in coordination as they move from the environment to the host and from one host niche to another. (cdc.gov)
Two of these methods, signature-tagged mutagenesis and in vivo expression technology, do not directly measure gene expression and do not allow true genomic-scale analysis, but they have been devised to identify genes necessary for pathogens during real infections. (cdc.gov)

Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. (biomedcentral.com)
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)
This can be achieved by counting the number of reads that align to each gene or by estimating transcript abundance using sophisticated algorithms. (pharmiweb.com)

However, with the development of gene expression profile and new high-throughput technology, the understanding of the pathogenesis of MDS is getting further and better. (frontiersin.org)
The identification of a COVID-19 host response signature in blood can increase the understanding of SARS-CoV-2 pathogenesis and improve diagnostic tools. (cdc.gov)

9. Analysis of gene expression by two-dimensional gel electrophoresis / A. M. Tolkovsky -- 10. (edu.au)

Although the utility of these prognostic assessment systems has been confirmed in clinical practice, they do not take gene mutations into account ( 13 ). (frontiersin.org)
Zhang Y, Hao S, Gao Y, Sun W, Li Y. Decoding Immune Heterogeneity of Melanoma and identifying immune-prognostic hub genes. (jcancer.org)

However, M1-type macrophages had a negative correlation with the hub genes. (biomedcentral.com)
Guided by these and other preliminary data, this project will address the gap in our current knowledge of how ISGs control Toxoplasma in pig cells by systematically identifying which and how the differentially expressed ISGs directly control Toxoplasma in pig macrophages using pig pluripotent stem cell-derived macrophages and high throughput ISG functional screening tools that we have recently developed. (usda.gov)
Unsensitized animals challenged with TMA exhibited also an increased number of macrophages in BAL, but gene expression in the above-mentioned gene pathways was unchanged or down-regulated. (cdc.gov)

In addition to quantifying gene expression, data coming from RNA-Seq allow for the discovery of new transcripts, the identification of alternative splicing events, the detection of allele-specific expression, and the detection of post-transcriptional alterations. (unict.it)
Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson's r = 0.92) and Ion Torrent Proton (Pearson's r = 0.92). (biomedcentral.com)
Extensive experimental results on simulation data and gene expression data sets demonstrate that our method can get higher identification accuracies than others. (scienceopen.com)
The hub genes were validated using external data (GSE764 and GSE68295). (biomedcentral.com)
In recent years, the advancement of bioinformatics has revolutionized gene expression analysis by providing powerful tools for data management, integration, and interpretation. (heartofamericanorthwest.org)
The generated data contain information about which genes are actively transcribed in both healthy individuals and those affected by the disorder. (heartofamericanorthwest.org)
Analyzing these data provides valuable information on which genes are upregulated or downregulated in lung cancer patients compared to healthy individuals. (heartofamericanorthwest.org)
This investigation used two databases to obtain expression data for PAAD patients. (hindawi.com)
Our objectives are, on these data, to decrease false discoveries when formally assessing the genes relative to a fold change threshold, and to provide a guided selection in the choice of this threshold. (biomedcentral.com)
Gene-wise statistical analyses of gene expression data, for which the significance relative to a fold change threshold is important, give reproducible and reliable results on NanoString data of mouse odorant receptor genes. (biomedcentral.com)
Because it can be difficult to set in advance a fold change threshold that is meaningful for the available data, we developed methods that enable a better choice (thus reducing false discoveries and/or missed genes) or avoid this choice altogether. (biomedcentral.com)
This set of tools may be useful for the analysis of other types of gene expression data. (biomedcentral.com)
The simultaneous analysis of the expression of thousands of genes in these high-throughput approaches challenges statistical methods and data interpretation. (biomedcentral.com)
In parallel, we used a version of the SMART-Seq2 protocol to obtain deep sequencing data (4-7,000 genes/cell) from 400 mitotic progenitors. (authorea.com)

In many high-throughput studies, genes are accepted as differentially expressed only if they satisfy simultaneously a p value criterion and a fold change criterion. (biomedcentral.com)

D3E is a method for identifying differentially expressed genes from single-cell RNA-seq experiments. (sanger.ac.uk)
The traditional statistical method for identifying DE genes between two samples is the student's t-test. (biomedcentral.com)

DGE analysis elucidates how genes respond to environmental stimuli, such as heat stress, chemical exposure, or pathogen infection. (pharmiweb.com)
orthogonal exPeriMental changes and pathways induced by EGE investigated the impact of aSSeSSMent of ePigenetic environmental factors in cancer causation, both current H. pylori infection and driver geneS and their link to underpinning studies of etiology e , pigenetic memory of past (eradicated) environMental carcinogenS carcinogen evaluation, and prevention. (who.int)

Quantitative reverse transcription polymerase chain reaction (qRT-PCR): qRT-PCR is a widely adopted method for quantifying gene expression levels due to its accuracy and sensitivity. (heartofamericanorthwest.org)
The scanner that records the intensity value is linked to digital image analysis software, which produces a color-coded image of the array, and a quantitative value is recorded for each target gene. (medscape.com)

Finally, there is only one expression profile of GSE47063 in terms of homo sapiens-based CRPS from the Gene Expression Omnibus (GEO) database, which included four patients and five controls. (iasp-pain.org)
Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
METHOD: The datasets GSE61592 (three MIRI and three sham samples) and GSE160516 (twelve MIRI and four sham samples) were selected in the Gene Expression Omnibus (GEO) database. (bvsalud.org)

Functional annotations revealed that these genes were mainly related to immune system activation and the processes of immunoreaction. (jcancer.org)

D3E compares the full distribution between two sample to identify a set of differentially expressed genes. (sanger.ac.uk)
Unsupervised hierarchical clustering was used to identify samples with similar expression profiles. (urotoday.com)
Hypergeometric analysis was used to identify canonical pathways and curated networks having statistically significant enrichment of differentially expressed genes. (urotoday.com)
Whole blood RNA-seq was used to identify differentially expressed lncRNAs. (lu.se)
Whole blood RNA-seq was used to identify differentially expressed lncRNAs and mRNAs in a cluster compared with all others. (lu.se)

Both metals perturbed gene expression in pathways related to oxidative stress, metabolism, DNA damage, cell cycle, and inflammatory response. (cdc.gov)
BACKGROUND: This bioinformatics report attempts to explore the cross-talk genes, transcription factors (TFs), and pathways related to myocardial ischemia-reperfusion injury (MIRI) as well as the gut microbiome. (bvsalud.org)

The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq. (biomedcentral.com)
Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. (biomedcentral.com)
As one of the most widely used tools for transcriptome profiling, quantification of differential gene expression has played a pivotal role in the identification of pathway and gene-network interactions [ 1 - 3 ]. (biomedcentral.com)

Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. (biomedcentral.com)

This study aimed to screen the hub genes and the immune cell infiltration pattern in ULMS by bioinformatics methods. (biomedcentral.com)
Interestingly, it indicated that 72 genes were mainly involved in immune processes and the Neddylation pathway. (biomedcentral.com)
These hub genes may affect the occurrence of USML through immune-related and Neddylation pathways, providing molecular evidence for the treatment of USML in the future. (biomedcentral.com)
The microenvironments of the low- and high-risk groups were assessed using xCell, the expression of immune checkpoints was determined, and gene set variation analysis (GSVA) was performed. (hindawi.com)
Cell-mediated immune responses are initiated by T lymphocytes that are themselves stimulated by cognate peptides bound to MHC molecules on antig en-presenting cells (APC). (thermofisher.com)
Methods: We integrated and analyzed the expression profiles of immune-related genes (IRGs) in 65 RTK patients based on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. (aging-us.com)

Based on the obtained results, this study indicates a small group of genes that result up-regulated in the severe form of the disease. (unict.it)
The present study contributes to a growing body of work on gene expression signatures in bladder cancer. (urotoday.com)
This study was aimed to specify the cytotoxic effect of C. sativa -derived extracts on colon cancer cells and adenomatous polyps by identification of active compound(s) and characterization of their interaction. (nih.gov)
To illustrate the importance of gene expression analysis, consider a hypothetical case study involving cancer research. (heartofamericanorthwest.org)
Differentially expressed genes were validated in the Innovative Medicines Initiative DIabetes REsearCh on patient straTification (IMI DIRECT) study. (lu.se)
A recent study of the disparity in breast cancer mortality between AA and EA women concluded that differences in mortality are driven by higher hazard rates of breast cancer death in AA women, irrespective of ER expression [9]. (cdc.gov)

Identification of differentially expressed genes by suppression subtractive hybridization / Sejal Desai, Jason Hill and Stephanie Trelogan / [et al. (edu.au)

It involves reverse transcribing RNA into cDNA using specific primers targeting desired genes, followed by amplification through PCR cycles. (heartofamericanorthwest.org)

fraction and subsequent gene expression analysis revealed a number of myeloid-related genes that were differentially expressed. (nih.gov)
WGCNA analysis revealed a green-yellow module possessed the highest correlation with ULMS, including 1063 genes. (biomedcentral.com)

BCR/ABL + gene expression pattern was more heterogeneous and was most similar to ALL without known molecular rearrangements. (aacrjournals.org)
We also identified a set of 83 genes that were highly expressed in leukemia blasts from patients without known molecular abnormalities who subsequently relapsed following therapy. (aacrjournals.org)
Supervised analysis of kinase genes revealed a high-level FLT3 expression in a subset of cases without molecular rearrangements. (aacrjournals.org)
Two other kinases (PRKCB1 and DDR1) were highly expressed in cases without molecular rearrangements, as well as in BCR/ABL-positive ALL. (aacrjournals.org)

Expression of each miRNA machinery component strongly correlates with intratumoral T cell infiltration in nearly all human cancer types. (nature.com)
However, adenocarcinomas of the lung, and occasional breast, transitional cell and pancreatic carcinomas had moderate or high levels of HE4 expression. (nature.com)
Finally, we used western blot to preliminarily detect the hub genes in cell lines. (biomedcentral.com)
Annexin V Assay and fluorescence-activated cell sorting (FACS) were used to determine apoptosis and cell cycle, and RNA sequencing was used to determine gene expression. (nih.gov)
C. sativa compounds interact synergistically for cytotoxic activity against colon cancer cells and induce cell cycle arrest, apoptotic cell death, and distinct gene expression. (nih.gov)
Single-cell sequencing: With recent advances in technology, it has become possible to analyze gene expression at the single-cell level. (heartofamericanorthwest.org)
T-cell activation is generally self-limited as activated T cells express receptors such as PD-1 (also known as PDCD-1) that mediate inhibitory signals from the APC. (thermofisher.com)
Subsequent differentiation allows for rear- analysis of a set of mouse B lineage cell lines rep- rangements of the Ig light-chain (IgL) genes that replace the resenting defined stages of B cell development us- surrogate light-chain genes on the surface of the B cell [8]. (lu.se)
immature cell is then subjected to negative selection to delete grouped based on their previously defined pheno- self-reactive cells before it leaves the BM to enter peripheral typic features, and a gene expression pattern for lymphoid organs, where it becomes a mature B cell [9]. (lu.se)

the gene expression profile during B lymphoid differentiation. (lu.se)

The transient assay of selected genes resulted in a synergistic increase of EFA-enriched TAG accumulation in tobacco leaves. (researchsquare.com)

Anatomy26

Organisms16

Diseases4

Chemicals and Drugs70

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes101

Disciplines and Occupations4

Information Science8

Health Care3

DEGs22

Ontology4

Microarray12

Microarrays12

Signaling pathway2

Large number of genes1

Enrichment analysis1

Biomarkers6

Human genes3

Protein15

Dataset5

Specific genes2

Target genes2

Significantly4

Thousands of genes simultaneously1

RNAs3

Employed to identify genes1

Patterns6

Biosynthetic genes1

Upregulation2

Tumor2

Clusters2

Functional annotation2

MiRNAs5

Proteins13

Differential expression3

Prognosis4

Annotation1

Identifies1

Bioinformatics analysis1

Five hub genes1

Biosynthesis2

Genome6

Weighted gene co-expression network analysis1

MRNA3

Biological6

Candidate genes1

Challenge in gene expression studies2

Immunohistochemistry1

Tissues5

Mechanisms4

Pathogens3

Abundance3

Pathogenesis2

Electrophoresis1

Prognostic2

Macrophages3

Data14

High-throughput1

Identifying2

Infection2

Quantitative2

Omnibus3

Annotations1

Identify5

Pathways related2

Quantification3

Whole-transcriptome1

Immune6

Study6

Suppression1

CDNA1

Analysis revealed2

Molecular4

Cell9

Differentiation1

Assay1