Sets gene expression. Medical search. Frequent questions

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)
GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. (molcells.org)
It has become a prevalent technology, allowing an efficient genome-wide relative quantification of gene expression and, in particular, it is the method of choice to find differentially expressed genes between two or more biological conditions of interest. (frontiersin.org)
By integrating two datasets (GSE77459 and GSE92681) in the GEO database using the sva and limma packages of R, differentially expressed genes (DEGs) of pulpitis were identified. (researchsquare.com)
To identify key genes differentially expressed in the human retinal pigment epithelium (hRPE) following low-level West Nile virus (WNV) infection. (molvis.org)
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)
Based on differentially expressed genes, we identified 22 major temporal co-expression (TCoE) patterns of gene expression and revealed enriched gene ontology biological processes. (usda.gov)

Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. (nature.com)
The gene ontology and pathway enrichment of DEGs were performed by DAVID and Kyoto Encyclopedia of Genes and Genomes online analyses, respectively. (hindawi.com)
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)
Across cell types, these genes affect neuronal morphogenesis and neuronal communication, while neural progenitor cells show strong enrichment for development of the limbic system. (springer.com)
Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. (molcells.org)
To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. (molcells.org)
We also analyzed the impact of both the replicate number and library size on gene ontology (GO) enrichment analysis. (frontiersin.org)
In addition, gene set enrichment analysis shows 6 pathways that differ between high- and low-risk group. (techscience.com)
Then, the DEGs were analysed to identify biological pathways of dental pulp inflammation with Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA). (researchsquare.com)
The nCounter Low RNA Input Kit employs multiplexed target enrichment to linearly amplify mRNA transcripts, enabling gene expression analysis with 1 nanogram to 10 nanograms of sample inputs. (genomeweb.com)

In the present study, we use mRNA microarray to acquire differential expression profiles in human TAD tissues and non-TAD tissues. (hindawi.com)
While researchers once believed that only genes were transcribed into messenger RNA (mRNA), investigators have recently discovered that non-coding DNA is copied into mRNA as well. (sciencedaily.com)
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)
vated mRNA expression. (lu.se)
Changes in the expression (mRNA) of several genes of interest were measured by real-time PCR. (cdc.gov)

BACKGROUND: Gene set analysis (GSA) has become a successful tool to interpret gene expression profiles in terms of biological functions, molecular pathways, or genomic locations. (uky.edu)
Thoracic aortic dissection (TAD) is a catastrophic disease worldwide, but the pathogenic genes and pathways are largely unclear. (hindawi.com)
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)
By integrating different datasets from the Gene Expression Omnibus (GEO) database, we analysed a merged expression matrix of pulpitis, aiming to identify biological pathways and diagnostic biomarkers of pulpitis. (researchsquare.com)
Finding out or estimating what functions or biological processes a gene involves can help interpret and understand the biological metabolic pathways. (iastate.edu)
Protein-protein interaction and gene set variation analysis revealed distinct sets of coordinately regulated genes and pathways whose expression progressively change over the course of the disease. (nih.gov)
The RNA MAPK-PI3K Pathways panel provides a curated gene set to measure transcriptional activity of those pathways. (genomeweb.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)
This study expands our understanding of gene activity during oat seed maturation and provides plant breeders the means to change oat seed composition through targeted manipulation of key pathways. (usda.gov)
Two of these genes, arginase 1 and eotaxin 1 are the focus of continuing investigations in mouse models of asthma regarding differences in mechanistic pathways depending on the allergen. (cdc.gov)
Array studies provide candidate genes to identify common mechanistic pathways in the effector phase, as well as mechanistic pathways unique to individual allergens. (cdc.gov)

Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. (biomedcentral.com)
In the former case, a gene set corresponds to an ontology term (representing a function, process, or a cellular component) and collects all genes annotated by that term. (biomedcentral.com)
Unlike the commonly used clustering methods, which start the analysis directly with the expression profiles, we used both the background knowledge (Gene Ontology annotation) and expression profiles during the analysis. (iastate.edu)
First, gene expression data was annotated by some broad Gene Ontology (GO) terms, according to their positions in Directed Acyclic Graph (DAG) of GO. (iastate.edu)

GSA performs statistical tests for independent microarray samples at the level of gene sets rather than individual genes. (uky.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)
The progressive nature of these changes enabled us to develop a framework for calculating a disease progression score for individual genes. (nih.gov)

Calculating the similarity between gene expression patterns (co-expression degree) by using gene expression data has an important guiding function in understanding the relationship between the corresponding proteins of the gene, and can help to identify whether different proteins have same or similar functions and whether they can be composed as protein complexes or functional modules. (biomedcentral.com)
Genes encoding disrupted complementary interactors tend to be risk genes, and an interaction network built from these proteins is enriched for ASD proteins. (springer.com)
For decades, scientists have known that, despite its name, "junk DNA" in fact plays a critical role: While the coding genes provide blueprints for building proteins, which direct most of the body's functions, some of the noncoding sections of the genome, including regions previously dismissed as "junk," seem to turn up or down the expression of those genes. (stanford.edu)
But it's been unclear how certain noncoding regions influence gene-expression levels - that is, the number of times a gene is copied into RNA and used to make proteins. (stanford.edu)
Although non-coding RNAs fail to produce functional proteins, researchers believe that in some cases these RNAs may control gene expression. (sciencedaily.com)
Protein-protein interaction (PPI) networks and modules were constructed to identify hub genes with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape. (researchsquare.com)
Even interactions external to the body, such as encountering an intruder in one's territory, were enough to trigger specific genes to start producing new proteins in the fish's brains. (2newthings.com)
We have learned that genes in mammalian cells are transcribed into messenger RNAs (mRNAs), which are to be translated into polypeptides (proteins). (intechopen.com)
A new study by Mark Bedford, Ph.D. , professor of Molecular Carcinogenesis , and colleagues published in Molecular Cell sheds light on the mechanism by which TDRD3 - a protein that 'reads' epigenetic marks on chromosomal proteins - turns on certain genes. (mdanderson.org)
Chemical modification of these histones is one way that the cell regulates the packing and unpacking of the DNA and its associated proteins (collectively called chromatin), which in turn helps to determine whether a given gene is activated or repressed. (mdanderson.org)
The authors set out to find clues to TDRD3's function by looking for physical interactions between TDRD3 and other proteins in the cell. (mdanderson.org)
The researchers studied the two proteins in breast cancer cell lines, where they discovered that TDRD3 recruits TOP3B to active chromatin (where genes are turned on) that is marked by arginine methylation. (mdanderson.org)
Gene expression generally produces proteins, but there are also non-coding genes that produce RNA molecules (rRNA, tRNA). (lu.se)
Transcription factors are a group of proteins that are needed for a gene to start being copied to RNA, i.e. for transcription to start. (lu.se)
It is not only the genes that code for proteins that are methylated, but also parts of the DNA that code for regulatory functions (RNA molecules), which can have a greater effect than genes. (lu.se)
Thus, the genotype is a complete set of instructions on how that person's body synthesizes proteins and thus how that body is supposed to be built and function. (msdmanuals.com)
Genes vary in size, depending on the sizes of the proteins or RNA for which they code. (msdmanuals.com)

Some of these genes play a role in the expression of certain genes at specific times during the day or night, which helps set circadian rhythms. (medlineplus.gov)
Even if the DNA sequence - the set of genes - is the same in all cells, only certain genes are expressed, i.e. only information from certain genes is copied (transcribed) and used to build protein structures or regulate processes. (lu.se)

Raw microarray data is available in Gene Expression Omnibus (National Center for Biotechnology Information) with accession number GSE6085. (uky.edu)
Gene Expression Omnibus (GEO) is a database for gene expression profiling and RNA methylation profiling managed by the National Center for Biotechnology Information (NCBI). (wikipedia.org)
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)
Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
Infinium data for four matched tumor-normal pairs and a dilution series of a tumor cell line mixed with its paired normal cell line are available in NCBI's Gene Expression Omnibus with accession GSE11976 . (lu.se)

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)
For example, steroid and thyroid hormones directly bind to nuclear receptors, which induce expression of specific genes. (intechopen.com)
In other words, expression of specific genes might have relevance to pathogenesis of diseases. (intechopen.com)

We investigate the functional relevance of de novo missense variants, specifically whether they are likely to disrupt protein interactions, and nominate novel genes in risk for ASD through integrated genomic, transcriptomic, and proteomic analyses. (springer.com)
Utilizing our previous interactome perturbation predictor, we identify a set of missense variants that are likely disruptive to protein-protein interactions. (springer.com)
Similar evolutionary reasoning may explain why many people in malaria-prone parts of Africa carry gene variants linked to malaria resistance. (gnxp.com)
Polymorphic variants at regulatory elements can cause differential allelic expression (DAE), thus using DAE as a quantitative trait could help identify such variation. (springer.com)
Alternative splicing results in multiple transcript variants of this gene. (cancerindex.org)
Studies have identified variants in multiple genes that are associated with developing seasonal affective disorder. (medlineplus.gov)
To characterize identified variants and genes functionally, we rely on a broad repertoire of functional genomics methods , including CRISPR-Cas9, synthetic oligonucleotide libraries, and massively parallel reporter assays (MPRA). (lu.se)

0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of TAD. (hindawi.com)
We show that differential allelic expression is common among these 12 candidate genes and is comparable between breast and blood (fresh and transformed lymphoblasts) in a significant proportion of them. (springer.com)
Different statistical methods with varying selection criteria resulted in identification of similar candidate genes. (cdc.gov)
Array data are intended to provide candidate genes for hypothesis generation and further experimentation. (cdc.gov)

The early findings suggest space travel boosts methylation, the process of switching genes on and off. (upi.com)
Over 10 years ago, arginine methylation of histone tails was identified as an epigenetic mark that was linked to gene activation. (mdanderson.org)
DNA methylation is a chemical process that regulates the function of the genes. (lu.se)

Instead, the non-coding RNA was suspected to play a role in hGH gene regulation. (sciencedaily.com)
We explored the possible expression and regulation of selected OR and TASR genes in human orbitofrontal cortex of sporadic Alzheimer's disease (AD) and found that these are expressed and markedly downregulated at early stages. (diagenode.com)
The expression pattern did not follow disease progression suggesting regulation through epigenetic mechanisms. (diagenode.com)
Findings suggest MeCP2 might be implicated in OR and TAS2R genes expression regulation through interaction with H3K9me3, and as an early event, it may uncover a novel etiopathogenetic mechanism of sporadic AD. (diagenode.com)
Researchers have identified a host of factors involved in epigenetic control of gene expression and development, but many of the precise mechanisms underlying this type of regulation remain unclear. (mdanderson.org)
Most genes that have been implicated in seasonal affective disorder are active (expressed) in the brain, where they are involved in the regulation of circadian rhythms. (medlineplus.gov)
Continued studies focused on genes showing minimal changes in the TMA-induced model but with clear up-regulation in the ovalbumin model. (cdc.gov)

RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. (frontiersin.org)
We identified significant regional differential expression in AD brains compared with control brains including expression changes of genes previously implicated in AD pathogenesis, particularly with regard to tangle and plaque formation. (elsevierpure.com)
RNA extracted from mock-infected and WNV-infected cells was assessed for differential expression of genes using Affymetrix microarray. (molvis.org)

Researchers recently discovered a novel mechanism that works over an extensive genomic distance and controls the expression of human growth hormone (hGH) in the pituitary gland. (sciencedaily.com)
Researchers at the University of Pennsylvania School of Medicine recently discovered a novel mechanism that works over an extensive genomic distance and controls the expression of human growth hormone (hGH) in the pituitary gland. (sciencedaily.com)
While mutations to the hGH gene often lead to abnormal growth in children and adults, these mutations have provided researchers with key clues regarding the genomic areas that appear to control expression of the hGH gene. (sciencedaily.com)
At the genomic level, a 14,000 base-pair separation is equal to the size of 10 growth hormone genes lined end to end. (sciencedaily.com)
Nevertheless, the present study delivers a catalog of reference genes under varied experimental conditions for the coleopteran forest pest I. sexdentatus and paves the way for future gene expression and functional genomic studies on this species. (lu.se)

Using the newly released and larger ASC dataset, we confirm these observations and take them in several new directions: (1) By defining a set of genes encoding these disrupted protein interactors in ASD subjects and another for their siblings, we evaluate their expression patterns in developing brain from fetal to early postnatal development and within general cell types of brain tissue. (springer.com)
however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. (molcells.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)
This study demonstrates a functional connection between nuclear CK2 and gene expression in relation to cell proliferation. (bvsalud.org)

In addition to environmental factors, phenotypes can also respond to genetic perturbations in a plastic or homeostatic manner, which characterizes the potential of an organism to express phenotypes when genes mutate. (nature.com)
We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. (molcells.org)
We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. (molcells.org)
In our genome-wide association studies ( GWAS ) we combine unique sample materials with sets of advanced phenotypes. (lu.se)

We've known for a while that short tandem repeats, or STRs, aren't junk because their presence or absence correlates with changes in gene expression," Fordyce said. (stanford.edu)
Gene expression of eye diseases should be studied as early as postnatal weeks 1-2 to ensure that any changes in gene expression pattern during disease development are detected. (molvis.org)
Another hypothesis about the association of COVID-19 severity and mortality with elevated exposure to PM involves changes in gene expression (upregulation) of a cellular protein (the angiotensin-converting enzyme two or ACE-2 receptor) that provides the primary entry point for SAR-CoV-2 into specific types of cells [10]. (cdc.gov)

Several types of chemical modifications of the five major histone protein families give rise to a complex 'histone code' that signals the transcriptional machinery to turn genes on or off. (mdanderson.org)
Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2α to active gene loci, more abundantly in late G1 phase than in early G1, notably at transcriptional start sites of core histone genes, growth stimulus-associated genes, and ribosomal RNAs. (bvsalud.org)
Our findings reveal that nuclear CK2α complexes may be essential to facilitate progression of the cell cycle, by activating histone genes and triggering ribosomal biogenesis, specified in association with nuclear and nucleolar transcriptional regulators. (bvsalud.org)

Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. (nature.com)
We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. (biomedcentral.com)
We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. (biomedcentral.com)
Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. (biomedcentral.com)
Regulatory polymorphisms in cis-acting elements result in the unequal expression of alleles. (springer.com)
Differential allelic expression (DAE) in heterozygote individuals could be used to develop a new approach to discover regulatory breast cancer susceptibility loci. (springer.com)
We aimed to perform a more extensive evaluation of differential allelic expression between blood and breast in order to assess the potential usefulness of LCL and fresh blood in association studies, to identify regulatory polymorphisms related to susceptibility to breast cancer. (springer.com)
Other evaluations include gene set analysis and gene regulatory network inference. (news-medical.net)
one includes structural genes encoding enzymes that directly participate in the formation of anthocyanins and other flavonoids, and the other comprises regulatory genes controlling the transcription of structural genes. (scirp.org)

With this study, we've seen thousands and thousands of genes change how they are turned on and turned off,' added Mason , who's based at Weill Cornell Medicine, Cornell University's medical school. (scientificamerican.com)
With this study, we've seen thousands and thousands of genes change how they are turned on and turned off. (upi.com)
A chromosome contains hundreds to thousands of genes. (msdmanuals.com)

A classic example is the heat shock protein system, particularly Hsp90 , whose expression is environmentally plastic and increases under thermal stress, but buffers phenotypic changes induced by mutations to maintain homeostasis 2 , a process termed canalization 3 . (nature.com)
Developing a protein function module recognition method ECTG based on Topological Features and Gene expression data for Protein Complex Identification. (biomedcentral.com)
ECTG(Evolutionary Clustering Algorithm Based on Topological Features and Gene expression data for Protein Complex Identification). (biomedcentral.com)
This method is based on evolutionary algorithm (EA), which effectively fuses protein topology and gene expression data. (biomedcentral.com)
Finally, we integrate protein interactions and cell-type-specific co-expression networks together with published association data to implicate novel genes in ASD risk in a cell-type-specific manner. (springer.com)
Consistent with other studies, genes identified by disrupted protein interactions are expressed early in development and in excitatory and inhibitory neuronal lineages. (springer.com)
Disrupted protein interactions identify gene sets involved in risk for ASD. (springer.com)
Transcription factors attach to noncoding DNA, regulating the expression of protein-coding genes. (stanford.edu)
While the CD79b gene normally codes for a protein in blood lymphocytes, researchers discovered that CD79b appears to play a very different role in the pituitary gland. (sciencedaily.com)
They found that TDRD3 forms a complex with a protein called topoisomerase 3B (TOP3B), an enzyme that unwinds DNA and, in so doing, prevents DNA structures from forming that impede gene transcription. (mdanderson.org)
The protein encoded by this gene is a member of the Tyro3-Axl-Mer (TAM) receptor tyrosine kinase subfamily. (cancerindex.org)
What does this gene/protein do? (cancerindex.org)
Scope includes mutations and abnormal protein expression. (cancerindex.org)
Under developmental conditions, the Tubulin beta-1 chain (β-Tubulin) was the most stable reference gene, followed by translation elongation factor (eEF2) and ribosomal protein S3 (RPS3). (lu.se)
Nuclear expression of protein kinase CK2α is reportedly elevated in human carcinomas, but mechanisms underlying its variable localization in cells are poorly understood. (bvsalud.org)
Genes are segments of deoxyribonucleic acid (DNA) that contain the code for a specific protein that functions in one or more types of cells in the body or the code for functional ribonucleic acid (RNA) molecules. (msdmanuals.com)
Protein synthesis is controlled by genes, which are contained on chromosomes. (msdmanuals.com)
A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)

Functional annotation clustering of the microarray data showed that gene clusters involved in immune and antiviral responses ranked highly, involving genes such as chemokine (C-C motif) ligand 2 ( CCL2 ), chemokine (C-C motif) ligand 5 ( CCL5 ), chemokine (C-X-C motif) ligand 10 ( CXCL10 ), and toll like receptor 3 ( TLR3 ). (molvis.org)
A suitable reference gene selection is fundamental for quantitative gene expression analysis and functional genomics studies in I. sexdentatus. (lu.se)

Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks are highly conserved across environments. (nature.com)
Within each temporal pattern, there were sets of genes with expression patterns affected by oat genotype. (usda.gov)
The genotype (or genome) is a person's unique combination of genes or genetic makeup. (msdmanuals.com)
Whether and how a gene is expressed is determined by a complex interaction of multiple factors including genotype, gene expression, environmental factors (including illnesses and diet), and other factors, some of which are unknown. (msdmanuals.com)

Upon depletion of RBPJ using CRISPR/Cas9, we observed specific upregulation of Notch target gene expression. (mdpi.com)
Quantitative real-time PCR analysis revealed that ABA treatment around véraison resulted in the upregulation of genes encoding enzymes responsible for both general flavonoid and anthocyanin biosynthesis. (scirp.org)
Thus, increases in the total amount and composition ratios of petunidin- and malvidin-type anthocyanins were mainly caused by ABA-induced upregulation of uridine diphosphate glucose flavonoid glucosyl transferase , glutathione S-transferase 4, O-methyl transferase and flavonoid 3', 5' hydroxylase expression, resulting in the deep coloration of berry of skin. (scirp.org)

This happens when the defined sets aggregate genes highly correlated in terms of their expression, thus minimizing variance inside the sets, and maintaining variance between them. (biomedcentral.com)
Within each TCoE set, highly correlated transcripts, putatively commonly affected by genetic background, were clustered and termed genetic co-expression (GCoE) sets. (usda.gov)

This mechanism involves a newly discovered set of "non-coding RNAs" expressed in the vicinity of the hGH gene. (sciencedaily.com)
By examining the relationship between these non-coding RNAs and the hGH gene, researchers hope to understand how these remote regions impact hGH gene expression and dysfunction. (sciencedaily.com)

CONCLUSIONS: The simulation study and the real data application showed that the proposed gene set analysis provides a promising tool for longitudinal microarray analysis. (uky.edu)

It was suggested that Tgfβ1 could possibly act as a signaling molecule in controlling collagen gene expression and modulate ECM during ocular growth. (molvis.org)

Recent global analyses of gene transcripts revealed that specific transcription factors (TFs) and their networking systems physiologically correspond to the onset of human diseases, including cancer. (intechopen.com)
The pre-processing of scRNA-seq data involves quality control, correcting for batch-effect, and normalizing the data, followed by downstream analyses such as cell-clustering and trajectory and gene set analyses. (news-medical.net)
Seventeen of the 22 TCoE sets had GCoE sets with median heritabilities higher than 0.50, and these heritability estimates were much higher than that estimated from permutation analysis, with no divergence observed in cluster sizes between permutation and non-permutation analyses. (usda.gov)

RESULTS: We provide a robust nonparametric approach to compare the expressions of longitudinally measured sets of genes under multiple treatments or experimental conditions. (uky.edu)
Finally, we recommend to RNA-Seq practitioners the production of a pilot data set to strictly analyze the power of their experimental design, or the use of a public data set, which should be similar to the data set they will obtain. (frontiersin.org)
Total RNA was isolated from experimental sets and reverse-transcribed to cDNAs. (gbif.org)
Gene expression studies could be considered as one of the key experimental approaches for such purposes. (lu.se)
Twelve commonly used reference genes in Coleopterans were screened under different experimental conditions to obtain accurate and reliable normalization of gene expression data. (lu.se)

For clinical samples, the general purpose of gene set analysis of genome-wide expression profiles is to identify underlying disease-associated molecular processes, which can facilitate disease diagnosis and therapeutic intervention. (molcells.org)

But current models don't adequately explain where and when transcription factors bind to noncoding DNA to regulate gene expression. (stanford.edu)
To better understand the role of short tandem repeats in gene expression, the researchers stripped the mechanisms down to their basics: transcription factors and naked DNA. (stanford.edu)
To test whether the transcription of the locus control region and CD79b played a significant role in hGH expression in transgenic mice, Ho then inserted a special piece of DNA into the locus control region. (sciencedaily.com)
R-loop accumulation at a gene can prevent transcription, and these loops are also often sites of DNA breaks. (mdanderson.org)
The findings were validated further using real-time quantitative reverse transcription PCR (RT-qPCR)-based target gene expression analysis. (lu.se)
Transcription factors bind alongside the promoter and set off the gene expression. (lu.se)

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)
Phylogenetic marker gene 16S rDNA was amplified with eubacterial and archaeal universal primers and amplicons were sequenced on Roche 454 sequencing platform. (gbif.org)
Marker genes are then used to annotate cell clusters, and the clusters are analyzed based on the cellular composition. (news-medical.net)
Anaplastic large cell lymphomas (ALCLs) are distinguished from other lymphomas by their anaplastic cytology and constant membrane expression of the CD30 antigen (an activation marker for B or T cells). (medscape.com)

Then Rough sets theory was applied to generate rules that characterize every class so that the classifier can classify unknown genes or unclear genes into those broad GO classes. (iastate.edu)
Morphogen gradients induce sharply defined domains of gene expression in a concentration-dependent manner, yet how cells interpret these signals in the face of spatial and temporal noise remains unclear. (elifesciences.org)

A study led by researchers at Stanford Medicine have unraveled some of the mystery of how non-coding DNA changes the level of gene expression. (stanford.edu)

Chromosomes are structures within cells that contain a person's genes. (msdmanuals.com)
Genes are contained in chromosomes, which are in the cell nucleus. (msdmanuals.com)
A karyotype is a picture of the full set of chromosomes in a person's cells. (msdmanuals.com)

Gene set analysis for longitudinal gene expression data" by Ke Zhang, Haiyan Wang et al. (uky.edu)
Set-level classification of gene expression data has received significant attention recently. (biomedcentral.com)
The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. (biomedcentral.com)
Besides obvious benefits in the interpretability of the learned classifiers, the set-level approach is mainly motivated by the problem of high feature dimension contrasting with the low number of available samples, which has been characteristic of gene expression data analysis. (biomedcentral.com)
When transforming expression data from the gene level to the lower-dimensional gene-set level, some information is obviously lost. (biomedcentral.com)
Intuitively, this loss is minimized when the set-level representation preserves most of the variance of the original data. (biomedcentral.com)
The algorithm can effectively remove the noise data reflected by calculating the topological structure characteristic values in the PPI network through the similarity of gene expression patterns, and also properly use the information hidden in the gene expression data. (biomedcentral.com)
The used compound standard set was the CYC2008 data set. (biomedcentral.com)
Closed Set Mining of Biological Data. (uni-trier.de)
E-CAST: A Data Mining Algorithm for Gene Expression Data. (uni-trier.de)
We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. (molcells.org)
We provide this carefully phenotyped, laser capture microdissected intraindividual brain region expression data set to the community as a public resource. (elsevierpure.com)
The traditional methods of microarray data analysis are based on the assumption that genes with similar expression profiles share the similar functions or biological processes, or genes with similar functions or biological processes share the similar expression profiles. (iastate.edu)
This method gave reasonable results either on yeast cell cycle data set or Arabidopsis time-course data set. (iastate.edu)
BioQC performs quality control of high-throughput expression data based on tissue gene signatures. (bioconductor.org)
It can detect tissue heterogeneity in gene expression data. (bioconductor.org)
Micro- array data from the ovalbumin and TMA model of asthma were also compared to previous data using Aspergillus as allergen to identify putative asthma `signature genes', i.e. genes up-regulated with all 3 allergens. (cdc.gov)
We make use of high-resolution, high-throughput flow cytometry, advanced imaging techniques, gene expression data as well as crosslinking data from population based registries. (lu.se)
The simulated data set used in the publication is available here . (lu.se)

To characterize gene expression signatures in acute lymphocytic leukemia (ALL) cells associated with known genotypic abnormalities in adult patients. (aacrjournals.org)

The integrated advanced bioinformatics methods may provide a way to solve the disadvantages and identify the hub genes involved in TAD. (hindawi.com)

Multidrug resistant phenotype (positive Pgp expression) is associated with a poor prognosis. (medscape.com)

However, there is neither a robust oat reference DNA sequence nor sequences of its transcribed genes (its transcriptome). (usda.gov)
Using deeply sequenced libraries of transcribed genes we assembled an oat seed transcriptome. (usda.gov)
With this reference transcriptome we quantified gene expression during seed development of 22 diverse lines across six time points. (usda.gov)
We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. (bvsalud.org)

The analytical limitations of over-representation approaches can be overcome by aggregate score approaches, which assign scores to each annotated gene set based on all the gene-specific scores of the member genes. (molcells.org)

It is necessary to generate hypotheses about functions or biological processes for unknown genes to help design more meaningful experiments. (iastate.edu)
We identified 22 major temporal expression patterns of gene expression and were able to show that these patterns associated with biological processes. (usda.gov)

Some of the induced genes, such as CREM, CHOP, and MAP kinase phosphatase-1, may be components of a homeostatic response to excessive stimulation. (jneurosci.org)
Supervised analysis of kinase genes revealed a high-level FLT3 expression in a subset of cases without molecular rearrangements. (aacrjournals.org)

Normal gene expression variation is thought to play a central role in inter-individual variation and susceptibility to disease. (springer.com)

For genes encoding the disrupted interactions, we evaluate their expression patterns across developing brains and within specific cell types, using both bulk and inferred cell-type-specific brain transcriptomes. (springer.com)
This study is predicated on previous parallel research on the postmortem brains of the same six regions in 14 healthy elderly individuals, for which LCM neurons were similarly processed for expression analysis. (elsevierpure.com)
The complexity of the molecules involved reinforced the assumption that this was always a slow process, but researchers tracking gene expression in stickleback brains found that DNA may be more accessible than we understood. (2newthings.com)

Genetic variance in expression increases at 18 °C relative to 25 °C for most genes that have a change in genetic variance. (nature.com)
It really sets the bedrock for understanding molecular risks for space travel as well as ways to potentially protect and fix those genetic changes. (scientificamerican.com)
Because epigenetic changes are essentially reversible - unlike genetic changes - the starting point for the search for drugs is that epigenetically inactivated genes can be reactivated (and vice versa) if only the right molecule is added. (lu.se)

Cell heterogeneity is also assessed by analyzing the differential gene expression. (news-medical.net)

This method was used for an IL-2 stimulation study and significantly altered gene sets were identified. (uky.edu)
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)
Linear regression between 634 metabolites from mature seeds and the PC1 score of each of the GCoE sets showed significantly lower p-values than permutation analysis. (usda.gov)

In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. (biomedcentral.com)

By identifying differences in neuronal gene expression profiles between healthy elderly persons and individuals diagnosed with AD, we may be able to better understand the molecular mechanisms that drive AD pathogenesis, including the formation of amyloid plaques and neurofibrillary tangles. (elsevierpure.com)
Pinpointing the expression of factors that may play a role in AD pathogenesis provides a foundation for future identification of new targets for improved AD therapeutics. (elsevierpure.com)

Gene expression must be appropriately maintained to regulate development, differentiation, and proliferation of cells. (intechopen.com)

Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. (bvsalud.org)

In this study, we expression profiled histopathologically normal cortical neurons collected with laser capture microdissection (LCM) from six anatomically and functionally discrete postmortem brain regions in 34 AD-afflicted individuals, using Affymetrix Human Genome U133 Plus 2.0 microarrays. (elsevierpure.com)

The firm is also offering a gene expression panel for myeloid cell innate immune response in humans or mice, developed in partnership with Lisa Coussens of Oregon Health and Sciences University. (genomeweb.com)
The next step would then be to identify a similar or identical set of biomarkers in other animals used in vaccine research, and in humans. (elifesciences.org)
Humans have about 20,000 to 23,000 genes. (msdmanuals.com)

A total of 470 DEGs comprising 394 upregulated and 76 downregulated genes were found in pulpitis tissue. (researchsquare.com)
Our findings support the use of differential allelic expression in blood as a surrogate for breast tissue in future studies on predisposition to breast cancer. (springer.com)
We compared the distribution of allelic ratios of gene expression in fresh blood (B cells and total mononuclear cells), transformed lymphoblasts, and breast tissue from unmatched healthy individuals. (springer.com)
In contrast, different sets of genes were shown higher stability in terms of expression under tissue-specific conditions, i.e. (lu.se)

Here, we used quantitative real-time PCR, profiling the expression of 93 genes in single-cells from three different cell lines. (frontiersin.org)
Quantitative real-time PCR analysis of 23 genes was used to validate the microarray results. (molvis.org)

Although high-throughput sequencing technologies have provided many diverse expressed genes, different expression profiles in TAD provided various results and no reliable results have been identified up to now [ 6 - 8 ]. (hindawi.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)

Multidrug resistance gene (ie, MDR1 ) expression correlates with unfavorable cytogenetic aberrations and is responsible for poor response to chemotherapy and short survival time. (medscape.com)

Seventeen of the 22 temporal patterns included gene sets with median heritabilities higher than 0.50. (usda.gov)
Temporal expression patterns of oat avenanthramides and lipid biosynthetic genes were concordant with previous studies of avenanthramide biosynthetic enzyme activity and lipid accumulation. (usda.gov)

Immune escape is mainly caused by histocompatibility complex (MHC) class I, abnormal antigen signaling mechanism, immunosuppressive components (such as HLA-G), Fas and its ligands to activate apoptosis and overexpression of other immunosuppressive molecules, such as lymphocyte activation gene 3 (LAG-3), T cell immunoglobulin and mucin domain 3 (TIM-3) ( Steven and Seliger, 2018 ). (techscience.com)

In this setting, predictive classifiers are learned using the lower-dimensional set-level representation. (biomedcentral.com)
Given the entailed reduction in sample dimensionality, the set-level approach should lead to a decreased risk of overfitting potentially resulting in improved accuracy of induced predictive models. (biomedcentral.com)
In this paper we hypothesize that the lack of predictive accuracy improvements observed in the previous studies was due to the adoption of unsuitable types of gene sets. (biomedcentral.com)
To identify the most predictive genes we used a variable selection strategy. (frontiersin.org)
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)

Anatomy26

Organisms16

Diseases4

Chemicals and Drugs70

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes101

Disciplines and Occupations4

Information Science8

Health Care3

Differentially9

Enrichment10

MRNA5

Pathways11

Ontology4

Individual genes3

Proteins17

Certain genes2

Omnibus5

Specific genes3

Variants7

Candidate genes4

Methylation3

Regulation7

Differential expression3

Genomic5

Dataset2

Cell proliferation2

Phenotypes4

Changes in gene expression3

Transcriptional3

Regulatory9

Thousands of genes3

Protein18

Functional2

Genotype4

Upregulation3

Highly correlated2

RNAs2

CONCLUSIONS1

Signaling molecule1

Analyses3

Experimental5

Genome-wide expression profiles1

Transcription6

Marker4

Unclear2

Level of gene1

Chromosomes3

Data19

Characterize1

Bioinformatics methods1

Phenotype1

Transcriptome4

Aggregate1

Biological processes2

Kinase2

Susceptibility1

Brains3

Genetic3

Heterogeneity1

Significantly3

Interpretable1

Pathogenesis2

Regulate1

Chromatin1

Affymetrix1

Humans3

Tissue4

Quantitative2

High-throughput1

Algorithm1

Aberrations1

Patterns2

Apoptosis1

Predictive5