• 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 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)
  • Our approach was able to uncover a cohesive set of differentially expressed genes and novel members exhibiting previously studied differential profiles. (wustl.edu)
  • 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)
  • In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)
  • Using a false discovery rate of 0.05, a total of 1,497 differentially expressed genes were identified. (biomedcentral.com)
  • 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)
  • Results: A total of 978 genes were differentially expressed and enriched for pathways associated to immune function and the mitochondria. (kcl.ac.uk)
  • 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 R package was used for data mining and screening differentially expressed genes (DEGs). (hindawi.com)
  • In this study, a data mining strategy was used to obtain 2 microarray datasets of gastric cancer from the GEO database to identify differentially expressed genes (DEGs) associated with gastric cancer occurrence and progression. (hindawi.com)
  • RNA-seq offers several advantages over microarrays or RT-qPCR for detecting differentially expressed genes (DEGs). (biomedcentral.com)
  • If a preponderance of genes in any of these predefined groups of genes (gene sets) is coordinately differentially expressed, it may be reasonable to hypothesize that the biological characteristic upon which that gene set was defined is relevant to the experimental perturbation. (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)
  • The interactome is significantly enriched with genes differentially expressed in MPM tumors compared with normal pleura and with other thoracic tumors, genes whose high expression has been correlated with un-favorable prognosis in lung cancer, genes differentially expressed on crocidolite exposure, and ex-osomederived proteins identified from malignant mesothelioma cell lines. (cdc.gov)
  • cortex and hippocampus were dissociated, and the fluorescent cells FACS purified for transcriptome profiling by RNA-seq. (jneurosci.org)
  • Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. (biomedcentral.com)
  • The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq. (biomedcentral.com)
  • As one of the most widely used tools for transcriptome profiling, quantification of differential gene expression has played a pivotal role in the identification of pathway and gene-network interactions [ 1 - 3 ]. (biomedcentral.com)
  • We profiled the transcriptome, chromatin accessibility state, and heteroplasmy in cells from the eyes of a patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and from healthy control donors. (jci.org)
  • 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)
  • 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)
  • DAVID was used to perform the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis for the different expression genes (DEGs). (medscimonit.com)
  • Then, the DEGs were analysed to identify biological pathways of dental pulp inflammation with Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA). (researchsquare.com)
  • Liu Y, Zhang YZ, Imoto S . Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases. (google.com)
  • Gene Ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). (hindawi.com)
  • Gene ontology implicated the immune system, including interleukins 4 and 13, as well as antimicrobial peptides in this overexpression. (biomedcentral.com)
  • Bioinformatic analysis of the proteomic phenotypes revealed shared Gene Ontology (GO) terms and signaling pathways within the clusters of co-expressed proteins (see Tables 1-2 ). (lu.se)
  • Whole genome analysis of lung, sampled 24 hours after challenge, showed expression changes of not only genes belonging to several Gene Ontology groups with up-regulation of inflammatory-associated genes and those associated with lung remodeling but also genes involved in downsizing these processes. (cdc.gov)
  • For this, we used microarrays to compare the gene expression profiles of sexually mature to immature males. (biomedcentral.com)
  • Different gene expression patterns, shown by tools such as quantitative PCR, microarrays, and high-throughput RNA sequencing, reveal how organisms respond to different environments. (nature.com)
  • Conclusions: Microarrays are a powerful tool to identify biomarkers for obesity by analyzing differential gene expression profiles. (sages.org)
  • Methods: Peripheral blood from 149 healthy controls and 131 first episode psychosis patients was profiled using Illumina HT-12 microarrays. (kcl.ac.uk)
  • In the past decade, microarrays and RT-qPCR have been the primary tools for analyzing gene expression changes. (biomedcentral.com)
  • To demonstrate the utility of openSESAME, we used gene expression signatures of two biological perturbations to query a set of 75,164 human expression profiles that were generated using Affymetrix microarrays and deposited in GEO. (biomedcentral.com)
  • Genome-wide gene expression microarrays have found widespread use because of their high throughput and ability to measure the expression of tens of thousands of genes simultaneously. (biomedcentral.com)
  • DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. (medscape.com)
  • Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. (medscape.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)
  • Odorant binding proteins (OBPs) are involved in either olfactory or nonolfactory cue sensation depending on their spatial and temporal expression. (bioone.org)
  • In this study, we observed that the expression of anti-apoptotic BCL2 family genes, such as BCL2, BCL2L1, and MCL1, is highly varied in T-ALL patients, and inhibitors targeting proteins coded by these genes display differential. (lu.se)
  • At each maturation stage, expression of proteins affects the commitment to move to the next stage and cellular functions, such as rearrangement and expression of Ig genes. (lu.se)
  • Defects in genes and proteins important for B cell maturation cause primary immunodeficiencies (see IDbase ). (lu.se)
  • Ten DEGs, including 7 hub genes from PPI analysis, were confirmed by real-time PCR. (medscimonit.com)
  • A total of 470 DEGs comprising 394 upregulated and 76 downregulated genes were found in pulpitis tissue. (researchsquare.com)
  • Using the GSE19826 and GSE54129 datasets, a total of 550 DEGs were identified, including 248 upregulated and 302 downregulated genes. (hindawi.com)
  • Papaver species are known to produce a large variety of benzylisoquinoline alkaloids, with each species exhibiting a specific alkaloid profile, but only a few genes involved in the biosynthesis or regulation of these complex pathways are known so far. (wustl.edu)
  • The aim of this study was to identify the genes and pathways underlying the growth of the mouse sclera during postnatal development. (molvis.org)
  • 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)
  • Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. (frontiersin.org)
  • 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)
  • Conclusions: Our results identified gene expression changes correlated with symptom severity and showed that key pathways are modulated by positive and negative symptom dimensions. (kcl.ac.uk)
  • What pathways are this gene/protein implicaed in? (cancerindex.org)
  • Collectively, our data suggest that venetoclax resistance can be mediated through the enrichment of distinct gene signatures and cytokine signaling pathways. (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)
  • 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)
  • Unsensitized animals challenged with TMA exhibited also an increased number of macrophages in BAL, but gene expression in the above-mentioned gene pathways was unchanged or down-regulated. (cdc.gov)
  • The results showed that nine ZmCAMTA genes showed highly diversified gene structures and tissue-specific expression patterns. (frontiersin.org)
  • My work also focus to disentangle the relationship between below ground inter- and intra-kingdom microbial co-occurrence and interaction networks, patterns of functional gene profiles and its implication in understanding ecosystem processes in different microbial hotspots. (ufz.de)
  • When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. (biomedcentral.com)
  • Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expression alterations. (biomedcentral.com)
  • openSESAME is a tool for leveraging the growing body of publicly available microarray data to discover relationships between different biological states based on common patterns of differential gene expression. (biomedcentral.com)
  • These relationships may serve to generate hypotheses about the causes and consequences of specific patterns of observed differential gene expression. (biomedcentral.com)
  • However, a challenge for scientists performing genome-wide gene expression microarray analysis has been using these data to generate hypotheses about biological processes responsible for the patterns of differential gene expression associated with a particular trait or experimental variable. (biomedcentral.com)
  • 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)
  • We evaluate several microarray analysis methods and study their performance, finding that none of the methods alone identifies all observable differential profiles, nor subsumes the results obtained by the other methods. (wustl.edu)
  • Therefore, we propose a machine learning based methodology that identifies and combines the abilities of microarray analysis methods to recognize differential profiles. (wustl.edu)
  • The follicular status of F1 and F2 were further evaluated in terms of healthy and atretic conditions by investigating mRNA localization of identified genes. (biomedcentral.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)
  • GABRB2 mRNA expression level varied with germline genotypes, and with the gender of the parent in accord with the process of imprinting. (wikipedia.org)
  • In the present study, we use mRNA microarray to acquire differential expression profiles in human TAD tissues and non-TAD tissues. (hindawi.com)
  • Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy. (biomedcentral.com)
  • The integrated advanced bioinformatics methods may provide a way to solve the disadvantages and identify the hub genes involved in TAD. (hindawi.com)
  • Bioinformatics data mining of gene expression profiles using the Gene Expression Omnibus (GEO) database has led to identifying promising biomarkers associated with disease development [ 12 ]. (hindawi.com)
  • His interests include Bordetella molecular pathogenesis and gene expression bioinformatics. (medscape.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)
  • Gene expression analysis of these sequences in P. bracteatum, P. somniferum and P. somniferum 'Noscapine' exhibited 39 cDNAs showing differential expression coincident with morphine accumulation. (wustl.edu)
  • We also examined which genes may be critical for ATAA by performing the integrative analysis of our single-cell RNA sequencing data with publicly available data from genome-wide association studies. (nih.gov)
  • In addition, integrative analysis of our single-cell RNA sequencing data with public genome-wide association study data and promoter capture Hi-C data suggested that the erythroblast transformation-specific related gene( ERG ) exerts an important role in maintaining normal aortic wall function. (nih.gov)
  • This methodology was successfully applied to a study of inflammation and host response to injury data set derived from the analysis of longitudinal blood microarray profiles of human volunteers treated with intravenous endotoxin compared to placebo. (wustl.edu)
  • Protein & ubiquitination profiling scioUbi is a high-content protein expression and ubiquitination level analysis. (sciomics.de)
  • scioCyto : Cytokine profiling scioCyto is a high-content analysis service for multiplex cytokine and chemokine profiling on protein level. (sciomics.de)
  • c , Principal components analysis of the 24 samples, based on overall gene expression, demonstrating clear separation of clusters by neuron subtype. (jneurosci.org)
  • c , Heatmap of z -score normalized RPKM expression levels of the same genes which contain the splice events in a , preserving the ordering of rows as in a . d , Principal components analysis of the 24 samples, based on the overall splice events quantification, demonstrating clear separation of clusters by neuron subtype. (jneurosci.org)
  • A case/control differential expression analysis was performed, followed by correlation of gene expression with positive and negative syndrome scale (PANSS) scores. (kcl.ac.uk)
  • Total RNA was pooled for each group and time-point (1, 3, 6, and 14 DPI) to make 16 libraries, for analysis by Digital Gene Expression Tag Profiling (DGETP). (usda.gov)
  • Park H, Imoto S , Miyano S. Comprehensive information-based differential gene regulatory networks analysis (CIdrgn): Application to gastric cancer and chemotherapy-responsive gene network identification. (google.com)
  • 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)
  • High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death. (umassmed.edu)
  • Then, the relationship between the expression level of the core genes and the prognosis of gastric cancer patients was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA) database. (hindawi.com)
  • All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. (biomedcentral.com)
  • Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. (biomedcentral.com)
  • Differential expression analysis of ileal, transverse colon, and rectal biopsies were supplemented by a comparison of transcriptomes from platelets and leukocytes subsets, including CD4+, CD8+, CD14+, CD15+, and CD19+ cells. (biomedcentral.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)
  • Gene set enrichment analysis (GSEA) showed enrichment of cytokine signaling in all three cell lines which was supported by the phospho-kinase array where STAT5 phosphorylation was found to be elevated in resistant cells. (lu.se)
  • Interactome analysis of diseaseassociated genes is a powerful approach with high translational impact. (cdc.gov)
  • Background: The causes of obesity are multifactorial and may include dysregulation of certain genes, such as peroxisome proliferator activated receptor gamma (PPAR gamma). (sages.org)
  • it is regulated via epigenetic regulation including imprinting and gene and promoter methylation GABRB2 has been associated with a number of neuropsychiatric disorders, and found to display altered expression in cancer. (wikipedia.org)
  • Multiple lines of evidence confirmed the epigenetic regulation of GABRB2 gene expression via methylation and imprinting. (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)
  • We observed a different trend of regulation in terms of BCL2 family gene expression and global gene expression profile including genes reported to be expressed in cancer stem cells. (lu.se)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
  • The growing volume of gene expression data in open data repositories such as the NCBI Gene Expression Omnibus (GEO) presents an opportunity to identify these gene expression similarities on a large scale across a diverse collection of datasets. (biomedcentral.com)
  • We have developed a fast, pattern-based computational approach, named openSESAME (Search of Expression Signatures Across Many Experiments), that identifies datasets enriched in samples that display coordinate differential expression of a query signature. (biomedcentral.com)
  • Known PPIs of the 62 MPM associated genes were derived from Biological General Repository for Interaction Datasets (BioGRID) and Human Protein Reference Database (HPRD). (cdc.gov)
  • The two successive nanos gene duplications may result from the second and third whole genome duplication events at the basis of Vertebrates and Teleosts respectively. (nature.com)
  • In teleostean fish, two nanos1 genes were generated, probably during the Teleost specific whole genome duplication (3R). (nature.com)
  • In this study, we first identified all the CAMTA homologous genes in the whole genome of maize. (frontiersin.org)
  • ATAA-related changes were then examined by comparing the proportions of each cell type and the gene expression profiles between ATAA and control tissues. (nih.gov)
  • Differential gene expression data suggested the presence of extensive mitochondrial dysfunction in ATAA tissues. (nih.gov)
  • GABRB2 is associated with a spectrum of neuropsychiatric disorders, and displays of differential gene expression between tumor and non tumor tissues. (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)
  • The two mRNAs expression profiles contained 13 TAD aortic tissues and 11 non-TAD tissues. (hindawi.com)
  • RNA sequencing is a powerful method to study differential gene expression because it can detect a whole gene expression across particular tissues 1 . (nature.com)
  • However, the landscape of heteroplasmy across cell types within tissues and its influence on phenotype expression in affected patients remains largely unexplored. (jci.org)
  • The rapid development of methods that select over/under expressed genes from RNA microarray experiments have not yet satisfied the need for tools that identify differential profiles that distinguish between experimental conditions such as time, treatment and phenotype. (wustl.edu)
  • The strength of evidence is compelling , using rigorous state-of-the-art methods to demonstrate functional redundancy of these genes in regulating the Lhx2/Lhx5 axis. (elifesciences.org)
  • Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. (biomedcentral.com)
  • Several independent high-throughput methods for differential gene expression (including SAGE and differential display) may enable function annotation of sequenced genomes [ 2 ] . (medscape.com)
  • 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)
  • Two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry (MS) based quantitative proteomics were used to study differential protein abundance in various B cell types during B cell maturation. (lu.se)
  • d , Heatmap of z -score normalized RPKM expression levels of genes significantly enriched in each neuron subtype. (jneurosci.org)
  • Here, we investigated, in females of both D. melanogaster and D. nigrosparsa , the gene expression between animals uninfected and infected with w Mel, using RNA sequencing to see if the two Drosophila species respond to the infection in the same or different ways. (nature.com)
  • Jones TI, Parilla M, Jones PL. Transgenic Drosophila for Investigating DUX4 and FRG1, Two Genes Associated with Facioscapulohumeral Muscular Dystrophy (FSHD). (umassmed.edu)
  • Neukomm LJ, Burdett TC, Gonzalez MA, Z?chner S, Freeman MR. Rapid in vivo forward genetic approach for identifying axon death genes in Drosophila. (umassmed.edu)
  • 0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of TAD. (hindawi.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)
  • Gene expression results echoed this course, as well as uncovered genes related to shared and unique host immune responses to the 3 viruses. (usda.gov)
  • Ileal mucosa in asthma exhibits a specific transcriptomic profile, which includes the overexpression of innate immune genes, mostly characteristic of Paneth and goblet cells, in addition to other changes that may resemble Crohn's disease. (biomedcentral.com)
  • Here, we have defined a set of genes that help to understand the molecular mechanisms controlling reproduction in eels. (biomedcentral.com)
  • Here, we performed comprehensive differential molecular profiling between TMJ fibrous and bony ankylosis. (medscimonit.com)
  • The recent identification of mammalian circadian clock genes now makes it possible to examine time zone adjustments from the perspective of molecular events within the suprachiasmatic nucleus (SCN), the principal circadian oscillator. (jneurosci.org)
  • These results reveal the potential for dissociation of mPer and mCry expression within the central oscillator during circadian resetting and a differential molecular response of the clock during advance and delay resetting. (jneurosci.org)
  • By understanding the molecular details of this interaction, we can identify virulence-associated microbial genes and host-defense strategies and characterize the cues to which they respond and mechanisms by which they are regulated. (medscape.com)
  • The pace of gene discovery rapidly accelerates, but its potential for explaining life at the molecular level remains largely unrealized because our understanding of gene function lags increasingly far behind. (medscape.com)
  • Novel PPIs were predicted by applying the HiPPIP algorithm, which computes features of protein pairs such as cellular localization, molecular func-tion, biological process membership, genomic location of the gene, and gene expression in microar-ray experiments, and classifies the pairwise features as interacting or noninteracting based on a random forest model. (cdc.gov)
  • This antimicrobial gene encodes a chemokine of the CXC subfamily and ligand for the receptor CXCR3. (cancerindex.org)
  • Here we examined 145 SNPs in 6 miRNA processing genes and in 78 miRNAs which target genes known to be important in breast cancer among 906 African American (AA) and 653 European American (EA) cases and controls enrolled in the Women's Circle of Health Study (WCHS). (cdc.gov)
  • Genes identified as involved in the main biologic processes during postnatal scleral development were further confirmed using qPCR. (molvis.org)
  • The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. (frontiersin.org)
  • The set of up-regulated genes includes genes involved in neuroendocrine processes, cell-cell signaling, neurogenesis and development. (biomedcentral.com)
  • Significant changes shared by the fly species belong to the expression of genes involved in processes such as oxidation-reduction process, iron-ion binding, and voltage-gated potassium-channel activity. (nature.com)
  • They showed that DF up-regulates genes regulating E 2 synthesis, anti-apoptosis, cell proliferation and gene transcription. (biomedcentral.com)
  • These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. (frontiersin.org)
  • We used the paradigmatic GATA-PU.1 axis to explore, at the systems level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. (lu.se)
  • thus, genomewide transcription profiling seems particularly appropriate for the study of this process. (medscape.com)
  • Dysregulation of PI3K/AKT can be triggered by activating mutations in a variety of genes, including RAS, PIK3CA , and AKT1, as well as by inactivation of PTEN . (medscape.com)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • Gene expression profiling in kidney cancer: combining differential expression and chromosomal and pathway analyses. (uchicago.edu)
  • One approach to this problem is to create sets of genes with common biological characteristics, such as chromosomal location, biochemical function, or observed differential expression in some experimental condition, and then to determine whether the genes in these sets are coordinately induced or repressed. (biomedcentral.com)
  • 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)
  • The rapid development of gene chip high-throughput sequencing technology has accumulated much disease-related data since the past ten years. (hindawi.com)
  • Based on phylogenetic and synteny analyses, this study reveals that nanos1 gene has undergone multiple duplications and gene copies losses in Vertebrates. (nature.com)
  • Our unique blood analyses confirm previous tissue data from our lab and shed new light on the ensuing cascade of gene dysfunction associated with obesity. (sages.org)
  • Enrichment analyses were performed on the associated gene lists. (kcl.ac.uk)
  • Though accepted as the gold-standard for measuring gene expression, this method is lower throughput and not amenable to perform global expression analyses. (biomedcentral.com)
  • Here the authors use innovative approaches to combine spatial profiling with single cell transcriptomics to define tumor-proximal populations of fibroblasts that predict clinical outcome. (elifesciences.org)
  • Specifically, elevated expression of HIF-1a and podoplanin predicted worse outcome while inflammatory gene expression correlated with increased survival, suggesting future interventions targeting proximal fibroblast populations to mitigate against PDAC. (elifesciences.org)
  • Transcriptomic profiling of T-cell populations in non-muscle invasive and muscle invasive bladder cancer. (lu.se)
  • Current models of the clockwork posit interlocked transcriptional/post-translational feedback loops based on the light-sensitive Period ( Per ) genes and the Cryptochrome ( Cry ) genes, which are indirectly regulated by light. (jneurosci.org)
  • In this study, we investigated whether hypothalamic HTT expression causes transcriptional changes. (lu.se)
  • MicroRNAs (miRNAs) are an integral part of the post-transcriptional machinery of gene expression and have been implicated in the carcinogenic cascade. (cdc.gov)
  • Although obese individuals have an overwhelming preponderance of fat, many genes and their respective products are dysfunctional. (sages.org)
  • They can bind to the 3′ untranslated region (3′UTR) of target messenger RNAs (mRNAs) in order to regulate gene expression post-transcriptionally with no sequence specificity but by potential electrostatic interactions with the phosphate backbone of RNA 2 , 3 . (nature.com)
  • MicroRNAs (miRNAs) are small, noncoding RNAs that bind to the 3' UTR of target mRNAs, and silence gene expression by inducing degradation of target mRNAs or inhibition of protein translation [ 10 ]. (cdc.gov)
  • Results: We identified 97 upregulated genes and 125 downregulated genes with >1.5 fold change in obese patients versus controls. (sages.org)
  • Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson's r = 0.92) and Ion Torrent Proton (Pearson's r = 0.92). (biomedcentral.com)
  • Structural changes and neuropathology in the hypothalamus have been suggested to contribute to the non-motor manifestations of Huntington's disease (HD), a neurodegenerative disorder caused by an expanded cytosine-adenine-guanine (CAG) repeat in the huntingtin (HTT) gene. (lu.se)
  • In contrast, the ubiquitous expression of full-length mHTT in the BACHD hypothalamus moderately affects the transcriptomic profile. (lu.se)
  • scioPhospho combines the advantages of a robust and cost-efficient protein expression profiling using scioDiscover with information on phosphorylation status. (sciomics.de)
  • Knowledge about protein expression levels is of utmost importance to predict toxic effects, estimate adverse effects of drug candidates and to identify new drug targets. (sciomics.de)
  • Is the Subject Area "Protein expression" applicable to this article? (plos.org)
  • Differential protein expression was studied in eight human cell lines representing various maturation stages from early pre-B cell until terminally differentiated plasma cell (see Supplementary Table 1 ). (lu.se)
  • Here we used a genomic approach to discover genes responsible for the determination of a specific alkaloid profile. (wustl.edu)
  • At present, gene chip technology has a vital role in diagnosing gastric cancer and evaluating related gene expression [ 13 ]. (hindawi.com)
  • Differential exon usage and expression of potassium channels. (jneurosci.org)
  • Taken together, these data identify Nanos as primordial genes with highly conserved functions for both, the migration of the germinal cells and their maintenance in adults. (nature.com)
  • The goal of this study was to identify genes that may be involved in sexual maturation in experimentally matured eels. (biomedcentral.com)
  • This allows openSESAME to identify perturbations of gene expression that are due to phenotypic attributes that may not have been described in the sample annotation included in the repository. (biomedcentral.com)
  • By monitoring microbial gene expression, one can predict the functions of uncharacterized genes, probe the physiologic adaptations made under various environmental conditions, identify virulence-associated genes, and test the effects of drugs. (medscape.com)
  • 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)
  • In mice, the suppression of Nanos3 expression in PGC resulted in the complete loss of germ cells in both sexes 9 . (nature.com)
  • In mice, the corresponding Gabrb2 gene on chromosome 11A5 comprises 12 exons and 11 introns, and the two isoforms β2L and β2S from alternative splicing consisted of 512 and 474 amino acids respectively. (wikipedia.org)
  • 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)
  • We encode the results of this methodology in decision making association rules able to decide which method or method-aggregation is optimal to retrieve a set of genes exhibiting a common profile. (wustl.edu)
  • 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 results revealed differential effects of benzene metabolites on embryonic and adult HSCs. (cdc.gov)
  • Binding of this protein to CXCR3 results in pleiotropic effects, including stimulation of monocytes, natural killer and T-cell migration, and modulation of adhesion molecule expression. (cancerindex.org)
  • There was concordance of gene over- ( STAT1 , XBP1 ) and underexpression ( NELF , RARA ) in asthma and Crohn's disease ileum when our results were compared to another dataset (p = 3.66 × 10 -7 ). (biomedcentral.com)
  • Interestingly, functional improvements were not sustained beyond 9 weeks coincident with a loss of RFP reporter-gene expression and a near-complete loss of treatment-associated functional recovery by 6 months post-treatment. (bvsalud.org)
  • The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. (nbic.nl)
  • The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. (usda.gov)
  • and (4) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry. (lu.se)
  • In Vertebrates, three Nanos paralogous genes were described. (nature.com)
  • In Vertebrates, Nanos paralogous genes were associated to partial redundancies and specific functional evolutions. (nature.com)
  • Interestingly, a cluster of dysregulated genes regarding cell metabolism and lipid formation were identified. (sages.org)
  • We combined global ChIP-seq of GATA1, GATA2, and PU.1 with expression profiling during differentiation to erythroid and neutrophil line- ages. (lu.se)
  • Our study provides a comprehensive evaluation of the cellular composition of the ascending aortic wall and reveals how the gene expression landscape is altered in human ATAA tissue. (nih.gov)
  • The impact of KRAS expression levels on the emergence of drug tolerance in lung cancer. (otago.ac.nz)
  • 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)
  • This study uses microarray technology to evaluate differential gene expression profiles in obese patients undergoing bariatric surgery versus non-obese controls. (sages.org)
  • By comparing diseaseassociated versus druginduced differential expression profiles, we identified five potentially repurposable drugs, namely cabazitaxel, primaquine, pyrimethamine, trime-thoprim and gliclazide. (cdc.gov)
  • Research topic: Construct soil metagenomic libraries from forest and grassland soils along land use gradients and screen for fungal functional genes. (ufz.de)
  • A study of differential gene expression profiling of aggressive and nonaggressive follicular carcinomas identified 94 genes that distinguish follicular carcinomas from follicular adenomas (including PBP and CKS2 ) and 4 genes that distinguish aggressive follicular carcinomas from nonaggressive follicular carcinomas ( NID2, TM7SF2, TRIM2, and GLTSCR2 ). (medscape.com)