Gene expression profiling. Medical search. Frequent questions

The results provide evidence that genes involved in tissue remodeling and repair are differentially regulated in the lungs of obstructed smokers and suggest that they are potential therapeutic targets. (nih.gov)
Hypergeometric analysis was used to identify canonical pathways and curated networks having statistically significant enrichment of differentially expressed genes. (urotoday.com)
This study was aimed at determining the differential gene expression patterns of OBP genes in the developmental stages (larval, pupal, teneral) and differentially starved adults of Glossina brevipalpis (Newstead) collected from Shimba Hills National Park, Kenya. (bioone.org)
The two expression profile datasets were integrated and we found out coexpression of differentially expressed genes (DEGs) using bioinformatics methods. (hindawi.com)
With the development of the gene expression profile, comparisons of differentially expressed genes that participate in the regulation of pathophysiological conditions in pathological tissue and normal tissue were available and convenient, and mRNAs gene expression profiles have been carried out in many diseases including TAD [ 6 ]. (hindawi.com)
Then we downloaded another microarray dataset GSE52093 [ 9 ] and screened out the coexpression of differentially expressed genes (DEGs) between TAD patients and non-TAD patients. (hindawi.com)
The peroxisome proliferator- activated receptor gamma coactivator 1-alpha ( Ppargc1a ) gene was found to be involved in the networks generated using Ingenuity Pathway Studio (IPA) from the differentially expressed transcript cluster lists of week 2 versus 1, week 3 versus 2, week 6 versus 3, and week 8 versus 6. (molvis.org)
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)
However, between malaria infected and coinfected children there were 240 differentially expressed genes with 180 genes upregulated and 60 downregulated in the coinfected group. (biomedcentral.com)
Using a false discovery rate of 0.05, a total of 1,497 differentially expressed genes were identified. (biomedcentral.com)
Five genes that were differentially expressed between invasive and either benign or normal tissues were validated by real time PCR in an independent panel of 46 serous tumors (4 benign, 7 LMP, 35 invasive). (biomedcentral.com)
Measurements and Main Results: Compared with control diaphragms, microarray analysis identified 354 differentially expressed, unique gene products after 6 and 18 h of mechanical ventilation. (syr.edu)
Statistical analysis identified 163 differentially expressed genes: 61 genes under-expressed in cancer and 102 genes over-expressed in cancer. (gatech.edu)
Expression levels in borderline tumours were intermediate between benign adenomas and malignant adenocarcinomas for a significant portion of the differentially expressed genes, suggesting that borderline tumours are a transitional state between benign and malignant tumours. (gatech.edu)
In this study, we tried to identify differentially expressed genes between largest (F1) and second-largest follicles (F2), and classify them by global gene expression profiling using a combination of microarray and quantitative real-time PCR (QPCR) analysis. (biomedcentral.com)
The mHTT and wtHTT groups showed the highest number of differentially expressed genes compared to the BACHD mouse model. (lu.se)
In BACHD mice, few hypothalamic genes were differentially expressed compared to age-matched WT controls. (lu.se)
Between late pregnancy (135 days of gestation ± 2.4 SD) and lactation (15 days post partum ± 1.27 SD) 13 % of genes in the sheep genome were differentially expressed in the ovine mammary gland . (bvsalud.org)

A popular approach to class discovery involves grouping similar genes or samples together using one of the many existing clustering methods such the traditional k-means or hierarchical clustering, or the more recent MCL. (wikipedia.org)

Notably, a large number of stress-related elements present in the promoter regions of some ZmCAMTA genes, indicating a genetic basis of stress expression regulation of these genes. (frontiersin.org)
CAMTAs participate in gene expression regulation by binding to the cis -elements in the promoter regions of numerous target genes. (frontiersin.org)
Subject: Gene Expression Regulation / Publisher: Cold Spring Harbor Laboratory. (nih.gov)
The higher expression of gremlin 1 and HIF1a genes after exposure to dragonfly larvae indicated an in vivo hypoxic reaction, while down-regulation of syndecan-2 may indicate impairment of angiogenesis. (biomedcentral.com)
Furthermore, functions assigned to mouse and human RPE expression profiles indicate (patho-) biological differences related to AMD, such as oxidative stress, Bruch's membrane, immune-regulation and outer blood retina barrier. (vu.nl)
Gene Expression Regulation, Developmental" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (jefferson.edu)
This graph shows the total number of publications written about "Gene Expression Regulation, Developmental" by people in this website by year, and whether "Gene Expression Regulation, Developmental" was a major or minor topic of these publications. (jefferson.edu)
Below are the most recent publications written about "Gene Expression Regulation, Developmental" by people in Profiles. (jefferson.edu)
Coordinated transcriptional regulation of large numbers of genes is required to switch between mammary tissue establishment during late pregnancy , and activation and maintenance of milk production during lactation . (bvsalud.org)
Our findings indicate the remarkable plasticity of the mammary gland , and the coordinated regulation of multiple genes and pathways to begin milk production . (bvsalud.org)

We analyse two comprehensive transcriptome datasets from human tissues and human-derived cell lines in terms of the expression profiles of the SLC and ABC families of membrane transporters. (biorxiv.org)
To meet multiple research goals, we offer a complete range of arrays for whole-transcriptome-, gene-, exon-, or short noncoding (snc)RNA-level analysis. (cd-genomics.com)
In conclusion, we show that both wtHTT and mHTT overexpression change hypothalamic transcriptome profile, specifically mHTT, altering neuroendocrine circuits. (lu.se)

The gene ontology and pathway enrichment of DEGs were performed by DAVID and Kyoto Encyclopedia of Genes and Genomes online analyses, respectively. (hindawi.com)

Plants, being sessile, have the ability to dramatically alter their gene expression patterns in response to environmental changes such as temperature, water availability or the presence of deleterious levels of ions. (nih.gov)
Characterisation of gene expression patterns in bladder cancer allows the identification of pathways involved in its pathogenesis, and may stimulate the development of novel therapies targeting these pathways. (urotoday.com)
The results showed that nine ZmCAMTA genes showed highly diversified gene structures and tissue-specific expression patterns. (frontiersin.org)
Given the uncertainty about the relationship between these different forms, we compared their patterns of gene expression. (biomedcentral.com)
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. (uchicago.edu)
Chemotherapy patients whose tumours exhibited benign-like expression patterns remained disease free for the duration of this study as indicated by continued normal serum CA-125 levels. (gatech.edu)
Differential expression patterns occurred between the normal and malignant tissue and correlated with histopathological parameters and overall surgical staging. (ul.ie)
However, little information is available on the gene expression profile (GEP) of CMV-CTL clones according to CMV reactivation patterns (and donor CMV serostatus) after allo-HCT. (nature.com)
This example shows a number of ways to look for patterns in gene expression profiles. (mathworks.com)
Expression patterns of these genes in other organs, namely muscle and propagation and fat tissues, were investigated by extracting RNA from the tissues. (animbiosci.org)
To analyze microarray datasets (34760 variables) and obtain functional implications of differential expression patterns, we used Linear Models for Microarray Data (limma) followed by Gene Set Enrichment Analysis (GSEA) using ClusterProfiler. (lu.se)

Genes involved in extracellular matrix synthesis/degradation and apoptosis were among the up-regulated genes, whereas genes that participate in antiinflammatory responses were down-regulated. (nih.gov)
Functional analyses indicated that some of the genes induced by dragonfly larvae caused an increase in laminins necessary for cell adhesion in the extracellular matrix. (biomedcentral.com)
We identified a panel of relevant extracellular matrix genes whose expression levels were measured by real-time quantitative polymerase chain reaction using Taqman VR reagents in twenty-four pairs of matched colorectal cancer tumour and associated normal tissue. (ul.ie)

Five OBP genes, GbrOBP2 , GbrOBP6 , GbrOBP7 , GbrOBP8 , and GbrOBP13 , were selected for quantitative PCR expression analysis as representatives of the three OBP classes in Glossina spp. (bioone.org)
Quantitative real-time PCR was used to test the expression of ZmCAMTA genes under several abiotic stresses (drought, salt, and cold), various stress-related hormones [abscisic acid, auxin, salicylic acid (SA), and jasmonic acid] and biotic stress [rice black-streaked dwarf virus (RBSDV) infection]. (frontiersin.org)
Here, we used quantitative real-time PCR, profiling the expression of 93 genes in single-cells from three different cell lines. (frontiersin.org)
QIAseq Targeted RNA Panels have been developed as a Sample to Insight solution for quantitative gene expression profiling using RNAseq. (qiagen.com)

DNA microarrays measure the relative activity of previously identified target genes. (wikipedia.org)
With the advent of microarrays allowing the expression levels of increasing numbers of genes to be quantified, gene expression profiling, microarray analysis and transcriptomics have become frequently used terms associated with sampling RNA from multiple different tissue types. (videolectures.net)
For this, we used microarrays to compare the gene expression profiles of sexually mature to immature males. (biomedcentral.com)
These diverse microarrays are designed based on the most recent genome content for generating genome-wide expression profiles of human, model organisms, plants, and animals. (cd-genomics.com)
Expression profiling was carried out on samples of 7 benign, 7 LMP and 28 invasive (moderate and poorly differentiated) serous tumors and four whole normal ovaries using oligonucleotide microarrays representing over 21,000 genes. (biomedcentral.com)
The authors used DNA microarrays to study temporal gene expression of almost all genes in Saccharomyces cerevisiae during the metabolic shift from fermentation to respiration. (mathworks.com)

At recruitment, whole blood was collected into Paxgene tubes from a subset of children for transcriptional profiling among uninfected (n = 12), S. haematobium infected (n = 16), malaria infected (asymptomatic, n = 8) or coinfected (n = 13) children. (biomedcentral.com)
In this study, we investigated whether hypothalamic HTT expression causes transcriptional changes. (lu.se)
Changes in the expression of epigenetic regulators, particularly chromatin remodellers, indicate a possible role in coordinating the large-scale transcriptional changes that appear to be required to switch mammary processes from growth and development during late pregnancy to synthesis and secretion of milk during lactation . (bvsalud.org)
We report that children who present with insulin-specific autoantibodies first have distinct transcriptional profiles from those who develop GADA autoantibodies first. (lu.se)
We have used transcript profiling to explore the early transcriptional responses of mature C. albicans biofilms exposed to various antifungal agents. (who.int)

This is due to alternative splicing, and also because cells make important changes to proteins through posttranslational modification after they first construct them, so a given gene serves as the basis for many possible versions of a particular protein. (wikipedia.org)
These profiles measure mRNA, not protein, so further studies are needed to corroborate that any detected changes in gene expression actually have meaning in the life of the cell. (genengnews.com)
Here we present ATAC with select antigen profiling by sequencing (ASAP-seq), a tool to simultaneously profile accessible chromatin and protein levels. (nature.com)
Fluoride exposure also significantly elevated the protein expressions of cytochrome c and active caspase-3. (greenmedinfo.com)
Transcriptomics has also expanded from sampling protein coding genes to non-coding transcripts such as miRNAs, which have the potential not only to act as more stable biomarkers, but also to regulate translation, and in themselves be used a therapeutic agents against specific targets. (videolectures.net)
Traditional bioinformatics methods including gene ontology (GO) and pathways enrichment analyses of DEGs combined protein-protein interaction (PPI) network and cytohubber calculating software as well as Molecular Complex Detection (MCODE) analysis were used to analyze the key gene and pathway. (hindawi.com)
the tadpoles showed reduced expression of cα(E)-catenin , small muscle protein, dystrophin , and myosin light chain genes. (biomedcentral.com)
In general, genes in the cell growth/cell maintenance, stress response, and nucleic acid metabolism categories showed predominant upregulation, whereas genes in the structural protein and energy metabolism categories were predominantly downregulated. (syr.edu)
The SEPTIN9 gene provides instructions for making a protein called septin-9, which is part of a group of proteins called septins. (medlineplus.gov)
Approximately 15 slightly different versions (isoforms) of the septin-9 protein may be produced from this gene. (medlineplus.gov)
Serum was collected for protein profiling. (cdc.gov)

The results of these studies have been used to investigate disease mechanisms, monitor progression of disease and identify specific genes or gene signatures which could be used as diagnostic or prognostic biomarkers. (videolectures.net)
Specific genes of relevance to malaria infection, including CD8a, were significantly downregulated in malaria-infected compared to coinfected children. (biomedcentral.com)
Expression of stage-specific genes in follicles may be closely associated with their growth or atresia. (biomedcentral.com)
By screening specific genes related to the muscle growth of swine using cDNA microarray technology, a total of 5 novel genes (GF (growth factor) I, II, III, IV and V) were identified. (animbiosci.org)
To determine the mechanism of muscle growth, further studies should be preceded using the 3 specific genes related to muscle growth, that is GF I, III, and V. (animbiosci.org)
The goal of our search was to identify publications describing the role of specific genes, gene signatures, or molecular pathways and their effects in response to environmental exposures. (cdc.gov)
In particular, exposure to CAS resulted in the upregulation of hypha-specific genes known to play a role in biofilm formation, such as ALS3 and HWP1. (who.int)

At the "Critical Assessment of Massive Data Analysis" conference held recently in Vienna, John Storey, from the Lewis-Sigler Institute for Integrative Genomics at Princeton University, gave a talk on dissecting the inflammatory complications in critically injured patients by within-patient gene-expression changes. (genengnews.com)
CD Genomics Provides high-resolution array scanning and automation to dramatically improve efficiency in gene expression. (cd-genomics.com)
To explore work on gene-environment interaction (GxE) at the Centers for Disease Control and Prevention (CDC) and the Agency for Toxic Substances and Disease Registry (ATSDR), we examined the CDC-Authored Genomics and Precision Health Publications Database (CDC-Authored GPHPD) , which includes articles published by CDC/ATSDR authors since 2011. (cdc.gov)

These profiles of plant response to environmental extremes (abiotic stresses) are expected to lead to regulators that will be useful in biotechnological approaches to improve stress tolerance as well as to new tools for studying regulatory genetic circuitry. (nih.gov)

The reviewer also asked question about gene set enrichment analysis, which I believe is written slightly confusing way. (peerj.com)
Gene Set Enrichment Analysis (GSEA) with leading-edge analysis showed that suppressed sterol- and cholesterol metabolism were shared between hypothalamic wtHTT and mHTT overexpression. (lu.se)
During lactation , high levels of milk fat synthesis were mirrored by enrichment of genes associated with fatty acid biosynthesis , transport and lipogenesis . (bvsalud.org)

In general, mRNA levels of ECM and collagen genes have been found to be downregulated in both the adult mouse sclera [ 6 ] and cornea [ 7 ] when compared with samples from an earlier developmental stage. (molvis.org)

Gene expression was related to forced expiratory flow between 25 and 75% of forced expiratory volume (FEF(25-75%) % predicted) revealing a signature gene set of 203 transcripts. (nih.gov)
With RNA-sequencing now becoming more affordable and with the advantages of identifying novel transcripts and detecting a greater range of expression levels, the future for gene expression profiling includes focusing on transcripts in specific cellular compartments, being an integral part of clinical trials and perhaps even a standard part of diagnostic procedures and therapeutic decisions. (videolectures.net)
Targeted RNA sequencing using UMIs is optimized to deliver highly reliable quantification down to ~100 copies of an RNA target in 25 ng total RNA (see figure Positive results with as little as 0.2 copies of RNA per cell ERCC standards, at 86 to 705,500 copies, spiked into universal reference RNA sample and enriched using 384-plex QIASeq Targeted RNA Panel in three technical replicates. (A) Sensitivity measurement. Under standard conditions (20 ng RNA input, 0.5 million MiSeq reads), ≥~100 copies of ERCC transcripts were reliability detected, which is the equivalent of ~0.2 copies per cell. (B) Precision measurement. At >10 barcodes/gene, CV was less than 5% for all targets, indicating high technical reproducibility. This corresponds to ~100 copies target RNA in the sample. "> Positive results with as little as 0.2 copies of RNA per cell ). (qiagen.com)
Methods of studying differential GENE EXPRESSION of especially low-abundance, tissue-specific gene transcripts. (bvsalud.org)

But even so, gene-expression profiling can be enormously valuable in finding biomarkers, highlighting druggable targets, revealing the metabolic pathways important in a biological process, and identifying subsets of a population that might respond to a certain therapy or be more susceptible to a certain clinical outcome. (genengnews.com)
This study involves a comprehensive, multi-modal, and integrative assessment of biomarkers implicated in the pathophysiology of PTSD, including measuring differences in whole-blood gene expression and other blood biomarkers of key neurobiological systems, an approach critical to informing risk and resilience prediction algorithms for PTSD, and to develop novel psychopharmacologic approaches for the treatment of this disabling condition in disaster responders and other trauma survivors. (cdc.gov)
0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of TAD. (hindawi.com)

The vast majority of RNA-seq studies are analyzed exclusively for differential gene expression (DGE). (ucdavis.edu)

Title : Impact of gene expression profiling tests on breast cancer outcomes Personal Author(s) : Marchionni, Luigi, M.D Corporate Authors(s) : Johns Hopkins University, Evidence-based Practice Center. (cdc.gov)
Survival curves for good prognosis (orange line) and poor prognosis (grey line) breast cancer patients according to 70-gene and 76-gene prognosis profiles are showed ( a and b , respectively). (biomedcentral.com)
Predicting continuous values of prognostic markers in breast cancer from microarray gene expression profiles. (lu.se)
High SEPT9_v1 expression in human breast cancer cells is associated with oncogenic phenotypes. (medlineplus.gov)

This study aims at integrating two gene expression profile datasets and verifying hub genes and pathways involved in TAD as well as exploring potential molecular mechanisms. (hindawi.com)
This paper analyzes gene expression datasets from cervical cancer microarray data. (peerj.com)
On the right of each survival plot, there are heat maps of the corresponding datasets, and the numbers represent the number of patients in each 20-gene score group. (biomedcentral.com)

Global gene expression profiles of F1 (10.7 +/- 0.7 mm) and F2 (7.8 +/- 0.2 mm) were analyzed by hierarchical cluster analysis and expression profiles of 16 representative genes were confirmed by QPCR analysis. (biomedcentral.com)
We demonstrated that global gene expression profiling of F1 and F2 clearly reflected a difference in their follicular status. (biomedcentral.com)
Whole blood cells, aorta and lung were harvested for global gene expression analysis with subsequent Ingenuity Pathway Analysis and confirmatory qRT-PCR. (cdc.gov)

The human genome contains on the order of 20,000 genes which work in concert to produce roughly 1,000,000 distinct proteins. (wikipedia.org)
While knowledge of the precise proteins a cell makes (proteomics) is more relevant than knowing how much messenger RNA is made from each gene,[why? (wikipedia.org)
Odorant binding proteins (OBPs) are involved in either olfactory or nonolfactory cue sensation depending on their spatial and temporal expression. (bioone.org)
Profiling the functional categories of co-ordinately expressed genes within this list revealed significant correlation between increased malignant potential and loss of both IGF binding proteins and cell adhesion molecules. (gatech.edu)
Loss of expression of IGF binding proteins as well as specific cell adhesion molecules may be a significant mechanism of disease progression in ovarian cancer. (gatech.edu)

It took me a long time to appreciate just how extensively population heterogeneity and other unmeasured sources of variation introduce unwanted and systematic biases into the statistical analysis of gene-expression studies," Dr. Storey noted. (genengnews.com)
Furthermore, microarray analysis was also utilized to characterize the effects of fluoride in gene expression profiling on mice sperm. (greenmedinfo.com)
Parts of the gene expression analysis market continue to develop in a somewhat predictable manner, whereas other segments are becoming increasingly complex and volatile. (kaloramainformation.com)
The interaction network analysis indicated that PTGS2, ICAM1, NOV and other genes may play a role in disc degeneration. (minervamedica.it)
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)
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)
Pathway analysis revealed substantial modulation of gene expression in defence and immune responses and in particular modulation of genes in the Fcγ-receptor-mediated phagocytosis pathway. (biomedcentral.com)
In this study, we examine gene expression changes through microarray analysis in spheroid versus monolayer ovarian cancer cells treated with TGFβ to induce EMT. (usf.edu)
Not unexpectedly, our gene expression analysis and comparative functional annotation suggested that, in general, the mouse and human RPE are very similar. (vu.nl)
Detailed analysis of cell cycle predictive genes allowed us to define subpopulations with distinct gene expression profiles and to calculate a cell cycle index that illustrates the transition of cells between cell cycle phases. (frontiersin.org)
Thus, an experimental setup for the comparative analysis between regenerative and nonregenerative conditions is essential to identify ideal targets for the promotion of regeneration-associated genes and to understand the mechanisms of axon regeneration. (korea.ac.kr)

To identify genes associated with neoplastic progression in the serous subtype of ovarian tumors, we compared gene expression in tissues that exhibited the spectrum of tumor behavior, namely benign, low malignant potential (LMP) and invasive. (biomedcentral.com)
Improved knowledge of gene expression changes and functional pathways associated with these clinical phenotypes may lead to new treatment targets, markers for early detection and a better understanding of disease progression. (gatech.edu)
We found that the total transcript level per cell and the expression of most individual genes correlated with progression through the cell cycle, but not with cell size. (frontiersin.org)

Hara Levy, professor of physiology at the Human and Molecular Genetics Center of the Medical College of Wisconsin, studies cystic fibrosis (CF). Although CF is caused by mutations in the CF transmembrane conductance regulator gene, patients with identical genetic mutations in this gene can suffer variable levels of lung disease severity. (genengnews.com)
Interestingly, both TGF-beta1 and SERPINE2 have been identified as candidate genes in COPD genetic linkage and association studies. (nih.gov)
Duplication of genetic material within the SEPTIN9 gene has also been identified in affected individuals. (medlineplus.gov)
More than half (23 of 39) of the articles represent epidemiologic studies including candidate gene and genome-wide association studies (GWAS) examining genetic effect modification on disease risk. (cdc.gov)

With no hypothesis, there is nothing to disprove, but expression profiling can help to identify a candidate hypothesis for future experiments. (wikipedia.org)
Unsupervised hierarchical clustering was used to identify samples with similar expression profiles. (urotoday.com)
The integrated advanced bioinformatics methods may provide a way to solve the disadvantages and identify the hub genes involved in TAD. (hindawi.com)
The aim of this study was to identify the genes and pathways underlying the growth of the mouse sclera during postnatal development. (molvis.org)
The goal of this study was to identify genes that may be involved in sexual maturation in experimentally matured eels. (biomedcentral.com)
Objectives: In these experiments, we used an Affymetrix oligonucleotide array to identify the temporal changes in diaphragmatic gene expression during controlled mechanical ventilation in the rat. (syr.edu)
Methods We performed a microarray study to identify and functionally annotate RPE specific gene expression in mouse and human RPE. (vu.nl)
To identify the most predictive genes we used a variable selection strategy. (frontiersin.org)
In conclusion, we provide useful experimental approaches and bioinformatics to identify informative and predictive genes at the single-cell level, which opens up new means to describe and understand cell proliferation and subpopulation dynamics. (frontiersin.org)
We will explore the distribution of SARS-CoV-2 and Flu reactive cells within gene expression clusters in the Barcode Enabled Antigen Mapping (BEAM) tutorial dataset and identify genes that are upregulated in these antigen reactive cells. (10xgenomics.com)
is used to identify the genes with missing data and indexing commands are used to remove the genes with missing data. (mathworks.com)
Here we use RNA-seq to identify differences in gene expression in the ovine mammary gland between late pregnancy and lactation . (bvsalud.org)

BACKGROUND: To investigate the microarray data on the gene expression profiles of intervertebral disc degeneration related to cytokine exposure. (minervamedica.it)

Conclusions: We conclude that mechanical ventilation results in rapid changes in diaphragmatic gene expression, and subsequently, many of these changes may contribute to atrophy and muscle fiber remodeling associated with unloading this primary inspiratory muscle. (syr.edu)

Immunohistochemistry confirmed expression of urokinase plasminogen activator (PLAU), urokinase plasminogen activator receptor (PLAUR), and thrombospondin (THBS1) by alveolar macrophages and airway epithelial cells. (nih.gov)

In the field of molecular biology, gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function. (wikipedia.org)

6 ], the transforming growth factor beta 1 ( Tgfβ1 ) gene and several collagen genes were significantly downregulated in 8-week-old B6 mice scleras when compared with 3-week-old B6 mice scleras. (molvis.org)

Genes in this pathway have been shown to be involved in the activation of transforming growth factor (TGF)-beta1 and matrix metalloproteinases and are subject to inhibition by SERPINE2. (nih.gov)
Genes associated with the classical complement pathway were downregulated in non-muscle invasive cancer. (urotoday.com)
Can testing of tumor tissue for mutations in EGFR pathway downstream effector genes. (cdc.gov)

This gene-expression profile provides substantially added value to conventional clinical markers, e.g., age, histological grade, and tumor size in predicting local recurrence despite radiotherapy. (lu.se)
The altered gene expression may enhance several cancer-related events such as cell division (proliferation), cell movement, and the development of new blood vessels (angiogenesis) that nourish a growing tumor. (medlineplus.gov)

BACHD mice with ubiquitous expression of full-length mutant HTT (mHTT) and wild-type mice with targeted hypothalamic overexpression of either wild-type HTT (wtHTT) or mHTT fragments. (lu.se)
In AAV groups, from the combined limma with GSEA using ClusterProfiler, we found both shared and unique gene sets and pathways for mice with wtHTT overexpression compared to mice with mHTT overexpression. (lu.se)

A highly distinct gene-expression profile for patients developing local recurrence after breast-conservation surgery despite radiotherapy has been identified. (lu.se)

Results Gene expression profiling (Affymetrix, U95Av2) was carried out on 18 ovarian tumours including benign adenomas, borderline adenocarcinomas of low malignant potential and malignant adenocarcinomas. (gatech.edu)

Understanding the interactions between our environment and our genes and how they affect health outcomes offers a multitude of potential opportunities in public health. (cdc.gov)

They showed that DF up-regulates genes regulating E 2 synthesis, anti-apoptosis, cell proliferation and gene transcription. (biomedcentral.com)

These genes were not expressed in the propagation and fat tissues, but were expressed in the muscle tissue. (animbiosci.org)

In developing a drug, one may perform gene expression profiling experiments to help assess the drug's toxicity, perhaps by looking for changing levels in the expression of cytochrome P450 genes, which may be a biomarker of drug metabolism. (wikipedia.org)
In other words, the scientist is making a specific prediction about levels of expression that could turn out to be false. (wikipedia.org)
Using mRNA from total blood leukocytes, they found that a full one-quarter of the human genome exhibits changes in expression levels during the early stages of post-trauma (40-80 hours post-trauma). (genengnews.com)
On the biological level, we demonstrate that gene expression levels fluctuate during in vitro development of both intracellular amastigotes and promastigotes. (cambridge.org)
Many ZmCAMTA genes displayed high expression levels in the roots. (frontiersin.org)
Predation-threat responsive genes were identified by selecting genes that reverted to control levels of expression following removal of the predator. (biomedcentral.com)
Interestingly, while genes involved in immune system function were down-regulated in the brains of mature males, changes in the expression levels of several receptors and channels were observed suggesting that some rewiring is occurring in the brain at sexual maturity. (biomedcentral.com)
Expression levels were measured at seven time points during the diauxic shift. (mathworks.com)
from the seven time steps in the experiment, the names of the genes, and an array of the times at which the expression levels were measured. (mathworks.com)
contains expression levels for YAL054C. (mathworks.com)
Innovative UMIs (unique molecular indices) eliminate PCR duplication and amplification bias to deliver the most accurate results (see figure Unbiased and accurate gene quantification (A) Different amounts (20 ng, 5 ng or 1.25 ng) of universal reference RNA were used to determine expression levels of three genes (BNIP1, CTNND2 and DAPK1) using targeted RNAseq. QIAseq digital RNA sequencing method (A; molecular barcode counts) showed accurate quantification of all three genes corresponding to different RNA input, whereas traditional targeted RNAseq (B; read counts) revealed PCR duplication limitation and yielded inaccurate quantification. "> Unbiased and accurate gene quantification ). (qiagen.com)

Multiple biosynthetic pathways such as sterol synthesis were among the top shared processes, where both unique and shared genes constituted leading-edge subsets. (lu.se)

Data are available at the Gene Expression Omnibus under accession number GSE156478 . (nature.com)
Overall, our analyses provide novel opportunities for the normalisation of genome-wide expression profiling data. (biorxiv.org)
3′ Tag-Seq is a protocol to generate low-cost and exceptionally low-noise gene expression profiling data. (ucdavis.edu)
We will investigate the clonality and diversity of lymphocytes within a non-small cell lung carcinoma sample, look at the distribution of clonotypes within two T cell phenotypes, and explore a well-conserved clonotype motif in the gene expression data. (10xgenomics.com)
Because barcoding happened before the sample was divided into V(D)J and Gene Expression libraries, the same cells appear in both data sets, and the barcodes match. (10xgenomics.com)
This example uses data from the microarray study of gene expression in yeast published by DeRisi, et al. (mathworks.com)
The full data set can be downloaded from the Gene Expression Omnibus website, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28 . (mathworks.com)
to show how many genes are included in the data set. (mathworks.com)
To make it easier to find the interesting genes, you can reduce the size of the data set to some subset that contains only the most significant genes. (mathworks.com)
One approach to dealing with these missing values would be to impute them using the mean or median of data for the particular gene over time. (mathworks.com)
This example uses a less rigorous approach of simply throwing away the data for any genes where one or more expression level was not measured. (mathworks.com)

We will combine our mRNAs expression profile (6 TAD tissues versus 6 non-TAD tissues) and GSE52093 downloaded from the Gene Expression Omnibus (GEO) database. (hindawi.com)

The limitations and possibilities associated with expression profiling in intracellular amastigotes and promastigotes were assessed through a series of comparative experiments in which technical and biological parameters were scrutinized. (cambridge.org)
We chose to use expression-curves rather than single, specific, time-point measurements to capture this biological variation. (cambridge.org)
Interestingly, in several instances co-ordinately expressed genes sharing biological function also shared chromosomal location. (gatech.edu)

A further 80 genes showed greater than 5 fold differences in expression after exposure to dragonfly larvae and 81 genes showed altered expression after exposure to larval salamanders. (biomedcentral.com)
In AMB-exposed biofilms, 2.7% of the genes showed altered expression, while in CAS-exposed biofilms, 13.0% of the genes had their expression modified. (who.int)

gene expression profiling provides the most global picture possible in a single experiment. (wikipedia.org)
Sometimes, a scientist already has an idea of what is going on, a hypothesis, and he or she performs an expression profiling experiment with the idea of potentially disproving this hypothesis. (wikipedia.org)
One key benefit of running an integrated 5' Gene Expression and V(D)J experiment is the ability to associate phenotypes with clonotypes of interest. (10xgenomics.com)
Typically, a gene expression dataset includes information corresponding to genes that do not show any interesting changes during the experiment. (mathworks.com)
Interestingly, FLU-exposed biofilms showed no significant changes in gene expression over the course of the experiment. (who.int)

his statistical challenge in this study was to correlate gene expression over multiple time points, in multiple patients, with multiple and different clinical presentations. (genengnews.com)
The present study contributes to a growing body of work on gene expression signatures in bladder cancer. (urotoday.com)
The purpose of this study was to develop a robust, standardized method for comparative expression profiling and molecular characterization of Leishmania donovani clinical isolates. (cambridge.org)
In this study, we first identified all the CAMTA homologous genes in the whole genome of maize. (frontiersin.org)
In the present study, we use mRNA microarray to acquire differential expression profiles in human TAD tissues and non-TAD tissues. (hindawi.com)
Since most of the genes examined here have orthologs in other vertebrates, the results of this study will contribute to the body of knowledge concerning reproduction in vertebrates as well as to an improved understanding of eel biology. (biomedcentral.com)
The aim of the present study was to use a novel, droplet-based, microfluidic platform to evaluate the prognostic value of a panel of thirty-four genes that regulate the composition of extracellular matrices in colorectal carcinoma. (ul.ie)
Several genes identified in this study will provide intriguing candidates for the determination of follicular growth. (biomedcentral.com)
Genes and pathways identified by the present study may be important for managing milk production and mammary development, and may inform studies of diseases affecting the mammary gland . (bvsalud.org)

Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell. (wikipedia.org)
Expression profiling is a logical next step after sequencing a genome: the sequence tells us what the cell could possibly do, while the expression profile tells us what it is actually doing at a point in time. (wikipedia.org)
Genes contain the instructions for making messenger RNA (mRNA), but at any moment each cell makes mRNA from only a fraction of the genes it carries. (wikipedia.org)
Many factors determine whether a gene is on or off, such as the time of day, whether or not the cell is actively dividing, its local environment, and chemical signals from other cells. (wikipedia.org)
In this genomic age, one possible answer is that a cell can be defined by a profile of all of the genes it is expressing. (genengnews.com)
Microarray technology and next-generation sequencing methods have enabled us to see all of the genes expressed by a given cell type at any particular time, or under a particular circumstance. (genengnews.com)
Such profiles can then be compared to those of other cell types, or the same cell type at other times or under other circumstances. (genengnews.com)
Recent technological advances have enabled massively parallel chromatin profiling with scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). (nature.com)
The Gini index (coefficient) characterises inequalities of distributions, and is used in a novel way to describe the distribution of the expression of each transporter among the different tissues and cell lines. (biorxiv.org)
Similar trends hold true for the expression profiles of transporters in different cell lines, suggesting that cell lines exhibit largely similar transport behaviour to that of tissues. (biorxiv.org)
PCBP1 is both reasonably highly expressed and has a low Gini coefficient in both tissues and cell lines, and is an excellent novel housekeeping gene. (biorxiv.org)
Given that the basic genome of a differentiated organism is constant between cells (and we here ignore epigenomics), what mainly discriminates one cell type from another is its expression profile. (biorxiv.org)
The set of up-regulated genes includes genes involved in neuroendocrine processes, cell-cell signaling, neurogenesis and development. (biomedcentral.com)
Over-expression of WNT7A in an ovarian cancer cell line led to increased migration and invasive capacity. (biomedcentral.com)
By applying the random forests algorithm, a supervised machine learning approach, we show how a multi-gene signature that classifies individual cells into their correct cell cycle phase and cell size can be generated. (frontiersin.org)
Here, we employed single-cell gene expression profiling to describe the dynamic transition between cell proliferative states in three different cell lines using a panel consisting of 93 marker genes. (frontiersin.org)
For more information on how to set up integrated V(D)J and gene expression experiments, go back to the Single Cell V(D)J + 5′ Gene Expression overview . (10xgenomics.com)
We have manually annotated this dataset in Loupe Browser, using gene markers (also saved with the dataset) to determine cell types. (10xgenomics.com)
For more information on how to create cell types using gene markers, visit the Exploring Substructure tutorial in the Loupe Browser documentation. (10xgenomics.com)
It is possible to load multiple V(D)J files for a single Gene Expression file to look at T cell clonotypes, B cell clonotypes, and gene expression profiles, all in the same view. (10xgenomics.com)
A skewed preference for BV7 genes and sequential "G" amino acids motif is observed in complementarity-determining region-3 of T cell receptor-β. (nature.com)
Single-cell RNA-sequence analyses demonstrate the homogenous distribution of the gene expression profile in individual cytomegalovirus-specific cytotoxic T-cells within each recipient. (nature.com)
On the other hand, bulk RNA-sequence analyses reveal that gene expression profiles among patients are different according to the cytomegalovirus reactivation pattern, and are associated with cytokine production or cell division. (nature.com)
An individual T-cell has a specific complementarity-determining region 3 (CDR3) of T cell receptor (TCR)-α and -β, which is a result of the recombination of somatic TCR V-(D)-J genes and junction diversity. (nature.com)
a cell array representing the gene names. (mathworks.com)

Conclusion Our findings indicate that gene expression profiling can reliably distinguish between benign and malignant ovarian tumours. (gatech.edu)

these often differ significantly from the 'housekeeping' genes commonly used for normalisation in transcriptomics and qPCR studies. (biorxiv.org)

Anatomy24

Organisms12

Diseases27

Chemicals and Drugs53

Analytical, Diagnostic and Therapeutic Techniques and Equipment55

Phenomena and Processes82

Disciplines and Occupations6

Technology, Industry, Agriculture2

Information Science10

Health Care10

Differentially23

Existing cluster1

Regulation10

Transcriptome3

Kyoto Encyclo1

Patterns11

Extracellular matrix3

Quantitative4

Microarrays6

Transcriptional5

Protein11

Specific genes7

Genomics3

Abiotic stresses1

Enrichment3

MRNA levels1

Transcripts4

Biomarkers3

Differential gene1

Breast cancer4

Datasets3

Global gene expression3

Proteins5

Analysis12

Progression3

Genetic4

Identify12

Microarray data1

Conclusions1

Epithelial1

Molecular biology1

Significantly downregulated1

Pathway3

Tumor2

Mice2

Distinct1

Affymetrix1

Outcomes1

Transcription1

Tissue1

Levels11

Synthesis1

Data11

Omnibus1

Biological3

Showed altered expression2

Experiment5

Study9

Cell25

Malignant1

Transcriptomics1