Datasets gene expression. Medical search. Frequent questions

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)
Adding together the number of datasets in the two major public data repositories, the National Center for Biotechnology Information's Gene Expression Omnibus and the gene-expression database at the European Bioinformatics Institute, the milestone should be reached within the next month. (the-scientist.com)
Analysis from the Gene Expression Omnibus datasets supported the mRNA findings. (hindawi.com)
The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. (nih.gov)
Investigators should submit data to the relevant NIH-designated data repository, e.g., dbGaP (for controlled access), the Single Nucleotide Polymorphism Database (dbSNP), GEO - Gene Expression Omnibus , or SRA - Sequence Read Archive , in a timely manner (see below). (nih.gov)
Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
Expression data are derived from records contained in the Gene Expression Omnibus , and are first log2 transformed and normalized. (yeastgenome.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)

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)
Results: We first show that scoring captures differential induction of damage or inflammatory pathways in a series of public datasets involving radiotherapy of colon adenocarcinoma, chemotherapy of breast cancer cells, replicative senescence of mesenchymal stem cells, and progression of melanoma. (gla.ac.uk)
Scoring of our own mesenchymal tumour dataset highlighted differential expression of secretory signalling pathways between distinct subgroups of MPNST, liposarcomas and peritoneal mesothelioma. (gla.ac.uk)
Conclusions: We find that "senescence scoring" accurately reports senescence signalling in a variety of situations where senescence would be expected to occur and highlights differential expression of damage associated and secretory senescence pathways in a context-dependent manner. (gla.ac.uk)
The high reproducibility of replicates, the strong concordance with a validation technique, and the coherent behavior observed for differentially expression features, both in terms of single genes and deregulated pathways, not only support the quality of the data, but also endorse their potential reuse. (unimi.it)
Pathway analysis of the significant genes showed that the genes were involved in known metastasis-associated pathways, such as integrin signaling, calcium signaling, and VEGF signaling. (nih.gov)
The objective of this work is to identify dysregulated genes and pathways of ccRCC temporally according to systematic tracking of the dysregulated modules of reweighted Protein-Protein Interaction (PPI) networks. (hindawi.com)
Finally, gene compositions of altered modules were analyzed, and pathways enrichment analyses of genes in altered modules were carried out based on Expression Analysis Systematic Explored (EASE) test. (hindawi.com)
We successfully identified dysregulated genes and pathways of ccRCC in different stages, and these might be potential biological markers and processes for treatment and etiology mechanism in ccRCC. (hindawi.com)
Delineating the pathogenesis of ccRCC by investigating the gene and epigenetic changes and their effects on key molecules and their respective biologic pathways is of crucial importance for the improvement of current diagnostics, prognostics, and drug development [ 4 ]. (hindawi.com)
In addition, a PPI network can be modeled as an undirected graph, where vertices represent proteins and edges represent interactions between proteins, to prioritize disease associated genes or pathways and to understand the modus operandi of disease mechanisms [ 9 , 10 ]. (hindawi.com)
IPA analysis of the 280 significantly differentially expressed genes in the whole blood was suggestive of increased hematopoiesis and cell development, activation of cancer/tumor development pathways, and atopy. (cdc.gov)
In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression-on the assumption that differential expression of key pathway genes may impact dose requirement. (biomedcentral.com)
We focus on 116 genes from the pharmacokinetic and pharmacodynamic pathways of warfarin within training and validation sets comprising both European and African-descent individuals. (biomedcentral.com)
Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. (lu.se)
Our objective is to analyze tumor gene expression data from microarrays in the context of such pathways. (lu.se)
For each dataset and many pathways we find a much larger number of significant samples than expected by chance. (lu.se)
rather, it is the result of the sequential and cumulative accumulation of mutations in key driver genes of signaling pathways. (bvsalud.org)
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)
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)
Two of these genes, arginase 1 and eotaxin 1 are the focus of continuing investigations in mouse models of asthma regarding differences in mechanistic pathways depending on the allergen. (cdc.gov)
Array studies provide candidate genes to identify common mechanistic pathways in the effector phase, as well as mechanistic pathways unique to individual allergens. (cdc.gov)
The project will identify key genes, pathways, and biological processes that are differentially regulated in response to hypoxia. (lu.se)

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)
The investigators combined eight microarray datasets from these brain regions and conducted a large-scale gene-expression analysis to probe for sex differences. (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)
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)
It is a main inductor of genes of antioxidant proteins and phase II detoxifying enzymes [ 1 ]. (hindawi.com)
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)
Bortoluzzi S, Alessi FD, Romualdi C, Danieli GA: Differential expression of genes coding for ribosomal proteins in different human tissues. (karger.com)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
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)
These SGM mutations frequently affect cancer tumor suppressor genes such as TP53 , FAT1 , and APC , keeping them from fully forming to produce proteins that prevent abnormal cells from growing and causing cancer. (medscape.com)

It is essential to exhaustively interrogate complex mRNA isoforms of protein-coding genes with an unified data resource. (nature.com)
In order to investigate representative mRNA transcript isoforms to be utilized as transcriptome analysis references, we utilized GTEx data to establish a top-ranked transcript isoform expression data resource for human protein-coding genes. (nature.com)
Therefore, information regarding reference annotated mRNA transcripts of respective human protein-coding genes would be beneficial for biomedical researches and pathological sequence variation analyses. (nature.com)
Furthermore, the miRNAs correlated negatively with the immunohistochemical expression of NRF1 and NRF2 but positively with their respective mRNA. (hindawi.com)
MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate gene expression by imperfect matching of mRNA [ 6 ]. (hindawi.com)
Because the locations of the probes are known, the intensity and pattern of the labeled mRNA can be used to measure the expression of the targeted gene. (medscape.com)
The CRC mRNA gene expression datasets from TCGA and GEO (GSE144259, GSE50760, and GSE87096) were analyzed to find the significant differentially expressed genes (DEGs). (bvsalud.org)

Gene expression profiles are essential in identifying different cancer phenotypes. (arxiv.org)
We adopted a "senescence scoring" methodology based on expression profiles of multiple senescence markers to examine the degree to which signals of damage-associated or secretory senescence persist in various human tumours. (gla.ac.uk)
Distinctive tissue specific expression profiles and modulations could be observed for individual top-ranked transcripts of protein-coding genes. (nature.com)
These studies provided us more information on the spliced transcript isoforms of protein-coding genes as well as more understanding on their expression profiles and translated protein products in human tissues and diseases. (nature.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)
When applying our approach, Regression2Net to gene expression and methylation profiles for individuals with glioblastoma multiforme, we identified, respectively, 284 and 447 potentially interesting genes in relation to glioblastoma pathology. (researchgate.net)
An excellent way to perform sophisticated queries of GEO data and to traverse links to other Entrez databases is to query Entrez GEO Profiles and Entrez GEO DataSets databases. (nih.gov)
Entrez GEO Profiles queries precomputed gene expression / molecular abundance profiles, while Entrez GEO DataSets queries all experimental annotation. (nih.gov)
Audic S, Claverie JM: The significance of digital gene expression profiles. (karger.com)
View genes with similar expression profiles using SPELL (Serial Pattern of Expression Levels Locator). (yeastgenome.org)
This diagram displays a gene network based on correlated expression profiles (purple lines) between the given gene (yellow circle) and genes that share expression profiles (gray circles). (yeastgenome.org)
Filter similar genes by adjusting the number of datasets in which their expression profiles are highly correlated with the gene of interest by clicking anywhere on the slider bar or dragging the tab to the desired filter number. (yeastgenome.org)
As we start to have more detailed environmental and lifestyle profiles of the patients in large cancer genomics datasets, we will be able to learn more about how mutations arise and how exactly these alter cells," he added. (medscape.com)
Using available RNA sequencing data from previously published studies on intestinal organoids, the project will compare the gene expression profiles with newly generated RNA sequencing data from our lab's organoid cultures at hypoxia. (lu.se)

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)
Third, we show how expression patterns of genes in a genomic interval might identify candidate genes in quantitative trait loci (QTL) mapping studies. (novartis.com)
GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. (nih.gov)
The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. (nih.gov)
In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. (researchgate.net)
First, penalized regressions are used to build Expression-Expression (EEnet) and Expression-Genomic or Expression-Methylation (EMnet) networks. (researchgate.net)
Seventeen ETV6/RUNX1-positive pediatric acute lymphoblastic leukemias were investigated by high-resolution array-based comparative genomic hybridization ( array CGH), gene expression profiling and fluorescence in situ hybridization. (lu.se)
Comparing the array CGH and gene expression patterns revealed that genomic imbalances conferred a great impact on the expression of genes in the affected regions. (lu.se)

Investigators used molecular methods to examine the expression of genes in three brain regions implicated in MDD: the dorsolateral prefrontal cortex, the subgenual anterior cingulate cortex, and the basolateral amygdala. (medscape.com)
Also, methods to examine sex-specific gene expression on a large scale have only recently been developed, he said. (medscape.com)
Different statistical methods with varying selection criteria resulted in identification of similar candidate genes. (cdc.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)

The identification of causal or predictive variants/genes/mechanisms for disease-associated traits is characterized by 'complex' networks of molecular phenotypes. (researchgate.net)
Alternative splicing results in multiple transcript variants of this gene. (cancerindex.org)
A field synopsis on low-penetrance variants in DNA repair genes and cancer susceptibility. (who.int)

These SNP effects may be population- and/or tissue-specific, and the Genotype-Tissue Expression (GTEx) datasets [ 11 ] make it possible to assess tissue-specific baseline levels of gene expression for specific ancestries. (biomedcentral.com)

Signaling through the type I IFN pathway leads to an increased expression of several IFN-responding genes (IRGs). (frontiersin.org)
Additionally, gene expression changes in the blood were indicative of ER-stress and downregulation of mTOR pathway. (cdc.gov)
Working within the gene or pathway level typically decreases the number of hypotheses [ 5 ] and may also bridge population-specific allelic compositions. (biomedcentral.com)
Moreover, we devise a score for pathway activity in individual samples, based on the average expression value of the downstream targets. (lu.se)
This approach defines a projection of high-dimensional gene expression data onto low-dimensional pathway activity scores. (lu.se)
This study shows that it is feasible to infer signal transduction pathway activity, in individual samples, from gene expression data. (lu.se)
The project aims to elucidate the impact of oxygen levels on the HIF-2α pathway and its target genes in the context of intestinal stemness and tissue renewal. (lu.se)

As a consequence, both factors are transported to the nucleus to induce the expression of their target genes. (hindawi.com)
By studying the expression profile and the proposed function of genes in the minimally gained region, several candidate target genes (SPANXB, HMGB3, FAM50A, HTATSF1 and RAP2C) were identified. (lu.se)
It will extend to the identification and characterization of HIF-2α target genes, with a specific emphasis on their role in modulating the fundamental processes associated with intestinal stemness and tissue renewal. (lu.se)

A feature selection process resulted in the identification of 12 candidate genes, which were subsequently reduced to 3 (CA2, CA7, and ITM2C) through gene expression and correlation analyses. (bvsalud.org)
Array data are intended to provide candidate genes for hypothesis generation and further experimentation. (cdc.gov)

dblp: Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. (dagstuhl.de)
Integration of gene expression and methylation to unravel biological networks in glioblastoma patients: Gadaleta et al. (researchgate.net)
In-depth biological analysis of connected genes in ANDnet and XORnet revealed genes that are related to energy metabolism, cell cycle control (AATF), immune system response, and several cancer types. (researchgate.net)
The involvement of these genes in CRC prognosis was further confirmed on the basis of their biological function and literature analysis. (bvsalud.org)
We provide courses in cutting-edge techniques and approaches for generating and working with large and complex biological datasets. (lu.se)
Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)

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)
Third, we performed a KEGG enrichment test of genes involved in biclusters to find evidence to support their functional consensus. (scirp.org)
Moreover, utilizing advanced bioinformatics tools, the project will employ Gene Set Enrichment Analysis (GSEA) to discern the enrichment patterns of HIF-2α target upregulated genes within the obtained datasets. (lu.se)

Gene composition analyses of altered modules revealed that there were 56 common genes (such as MAPK1 , CCNA2 , and GSTM3 ) existing in the four stages. (hindawi.com)
Examples of 2-omics analyses include expression quantitative trait locus eQTL (Franke & Jansen, 2009) and methylation quantitative trait locus meQTL (Smith, Kilaru, Kocak, Almli, & Mercer, 2014) that, respectively, assess the influence of genetic and epigenetic markers on gene expression. (researchgate.net)
The important features were further analyzed for gene expression, correlation, and survival analyses. (bvsalud.org)

2019). Differential expression of olfactory genes in Atlantic salmon (Salmo salar) during the parr-smolt transformation [Dataset]. (datadryad.org)

However, alternatively compounded patterns of human protein-coding gene transcripts would complicate gene expression data processing and interpretation. (nature.com)
Comprehensive investigation on the tissue expression patterns of top-ranked transcript isoforms is crucial. (nature.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)
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)
Once they determined the larger trends in gene expression following the damage, the UMSOM scientists then searched a database of FDA-approved drugs to find those that are known to produce opposite patterns of those caused by the noise. (newswise.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)
Previous data has reported similarity between human brain and testis gene expression patterns. (karger.com)
Hence, it means that human testis could also play a crucial role in human speciation if these two tissues exhibit similar gene expression patterns. (karger.com)
Determining the large scale anatomy of gene expression patterns of various human tissues could draw a more convincing conclusion, and better our understanding of the correlation/inter-correlation among different tissues. (karger.com)
Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. (karger.com)
Present results provide evidence to support the proposal that human testis and brain share the highest similarity of gene expression patterns. (karger.com)

Treatment of pre-smolts with triiodothyronine in vivo and ex vivo had, however, only subtle effects on the investigated olfactory targets, questioning the hypothesis that thyroid hormones directly regulate gene expression in the olfactory epithelium. (datadryad.org)

Recent discovery of several new markers allows for an expression profiling approach to study specific senescence phenotypes in relevant tissue samples. (gla.ac.uk)
For example, PrediXcan [ 10 ] imputes the expected baseline expression of a gene based on the allele composition of SNPs in proximity to that gene ( cis -SNPs) and uses these predicted baseline expression values to identify gene associations to disease phenotypes. (biomedcentral.com)

Here, we describe the loss and gain of function approaches experimentally used to modulate LEADR expression, and the bioinformatic procedures employed to analyze microarray data in our published article "LEADeR role of miR-205 host gene as long noncoding RNA in prostate basal cell differentiation" [1]. (unimi.it)

Clustering gene expression datasets can provide accurate identification of cancerous cell lines, but this task is challenging due to the small sample size and high dimensionality. (arxiv.org)
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)
Whole blood gene expression profiling is a promising approach to identification of novel biomarkers for tissues over traditional, invasive biopsy. (cdc.gov)
It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. (csc.fi)
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)
[ 2 , 3 ] Conventional techniques of gene investigation in cancer rely on the identification of single genetic alterations associated with disease. (medscape.com)
The introduction of complementary DNA (cDNA) microarray technology in 1995 has helped to facilitate the identification and classification of DNA sequence information and the assignment of functions to these new genes by allowing investigators to analyze expression of thousands of genes simultaneously in a single experiment. (medscape.com)

We constructed three joint datasets following three different strategies for dataset integration: in particular, using all common genes from the datasets, uncorrelated, and not co-expressed genes, respectively. (pharmb.io)

Supplementary Data 2: significantly enriched Gene Ontology categories of the pairwise comparisons using the Mann-Whitney U test. (figshare.com)
Supplementary Data 3: overlap of Gene Ontology Categories between different comparisons. (figshare.com)

Cluster analysis identified 3 gene expression signatures on the basis of IRF4 and IRGs expression which were differentially used by SLE and RA patients. (frontiersin.org)
We hypothesize that a meta-analysis of publicly available gene expression datasets in various tumor types can identify a signature of metastasis that is common to multiple tumor types. (nih.gov)
We performed a meta-analysis using a modified permutation counting method in order to obtain a common gene signature of metastasis. (nih.gov)
We then validated this signature in independent datasets using gene set expression comparison analysis with the LS-statistic. (nih.gov)
The meta-analysis of such datasets is, however, very complicated for various reasons. (pharmb.io)
Here, we developed an integrating statistical and machine-learning model approach for the meta-analysis of bisphenol A (BPA) exposure datasets from different mouse tissues. (pharmb.io)
Our results highlight the benefit of combining existing datasets for the integrated analysis of a specific topic when individual datasets are limited in size. (pharmb.io)
With more and more researchers conducting experiments that tease apart the functions of the thousands of genes that make up the genomes of mice, rats, and humans, the number of gene-expression datasets deposited in publicly accessible databases will soon reach 1,000,000, according to an analysis done by Nature . (the-scientist.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)
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)
The team added their newest data on noise-induced hearing loss to gEAR - Gene Expression Analysis Resource - a tool developed by her laboratory that allows researchers not trained in informatics to browse gene expression data ( published earlier this summer ). (newswise.com)
The teams then combined the datasets and performed their analysis. (newswise.com)
Users can restrict the data to particular cell types and can also divide the data into groups and perform a differential gene-expression analysis between the groups. (genengnews.com)
These evidences are often based on the derivation of standard measures of association, linking (epi-)genetic markers to gene expression combined with gene expression analysis (Wagner, Busche, Ge, Kwan, & Pastinen, 2014). (researchgate.net)
Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions. (lu.se)
Second, we conducted a bioinformatics analysis of gene-phenotype association matrix to identify gene modules (biclusters). (scirp.org)
X. Cui, Q. Sha, S. Zhang and H.-S. Chen, "A Combinatorial Approach for Detecting Gene-Gene Interaction Using Multiple Traits of Genetic Analysis Workshop 16 Rheumatoid Arthritis Data," BMC Proceedings, Vol. 3, Suppl. (scirp.org)
The PCL files generated for each dataset are used to populate the expression analysis tool SPELL . (yeastgenome.org)
Datasets are used to populate the expression analysis tool SPELL and may contain data for more than one unique experimental condition. (yeastgenome.org)
The scanner that records the intensity value is linked to digital image analysis software, which produces a color-coded image of the array, and a quantitative value is recorded for each target gene. (medscape.com)
The survival analysis showed a significant logrank p-value of 0.044 for the final gene signatures. (bvsalud.org)
The analysis of tumor immunocyte infiltration showed a weak correlation with the expression of the gene signatures. (bvsalud.org)
These genes were analyzed for survival and correlation analysis between final genes and infiltrated immunocytes. (bvsalud.org)
The overall survival analysis had finalized GLP2R and VSTM2A genes that were significantly downregulated in tumor samples and had a strong correlation with immunocyte infiltration. (bvsalud.org)
The analysis showed that in control individuals, expression of the examined genes was the same in men and women. (medscape.com)

Like other environmental pollutants, bisphenols are being tested in various experimental models, creating large expression datasets found in open access storage. (pharmb.io)
Via the "gene search" option, users specify a gene, brain region, and experimental platform to view the resulting data in graphical form. (genengnews.com)
The number of unique experimental conditions are indicated and all datasets are referenced. (yeastgenome.org)

The goal of this study was to look for correlates between RNA expression in lung tissue and in whole blood after MWCNT exposure. (cdc.gov)
The intensity of fluorescence is analyzed and correlates with expression of the gene. (medscape.com)

[ 1 ] the Cancer Genome Anatomy Project index of tumor genes has classified more than 40,000 genes directly or indirectly involved in one or more cancers. (medscape.com)

We investigated the expression of immune checkpoints (ICs) on lymphoid populations within the CRC TME and compared with cells from normal colon tissues using samples from 50 patients with varying disease stages. (mdpi.com)
14 ] combined PPI and gene expression data to construct tissue-specific PPI networks for 60 tissues and used them to prioritize disease genes. (hindawi.com)
Differential Gene Expression in Liver, Gill and Olfactory Tissues of Coho Salmon (Oncorhynchus kisutch) after Acclimation to Salinity. (nih.gov)
and (2) we impute genes only in tissues where expression quantitative loci (eQTLs) are associated with these genes. (biomedcentral.com)
We impute gene expression in specific tissues for each individual using the GTEx compendium [ 11 ] (Fig. 1 ) and learn a signature that is predictive of warfarin dose comprising gene-tissue pairs on a training cohort. (biomedcentral.com)

[ 5 ] Because a microarray can be used to examine the expression of hundreds or thousands of genes at once, it promises to revolutionize the way gene expression is examined. (medscape.com)

Expected and potentially novel resistance genes are enriched in the top hits and are validated using individual sgRNA as well as cDNA overexpression. (cdc.gov)

Gene-expression data can help scientists test preliminary hypotheses about which genes may contribute to the development of certain diseases, leading to potential drug targets. (the-scientist.com)
After making their study known to other researchers in their field, the team heard from scientists at Decibel Therapeutics (led by Joe Burns, PhD) and the Karolinska Institute (led by Barbara Canlon, PhD), who had the gene expression data from the inner ear's neurons, side wall and immune cells from before and after noise damage. (newswise.com)
By receiving robust datasets, computational scientists should be able to develop models that are "sensitive enough and specific enough that it doesn't matter [where] the data comes from," Julia Hoeng, director of systems toxicology for PMI R&D and PMI project leader of the SBV IMPROVER project, told GenomeWeb. (genomeweb.com)
A team that included scientists from Lagos, London and the U.S. found a previously unknown gene variant that can nearly quadruple the risk of Parkinson's for people of African ancestry. (cdc.gov)

d , Heatmap of z -score normalized RPKM expression levels of genes significantly enriched in each neuron subtype. (jneurosci.org)

The differential expression of IRF4 in RA was then confirmed in publicly available gene expression datasets. (frontiersin.org)

These significant genes were further processed for feature selection through boruta and the confirmed features of importance (genes) were subsequently used for ML-based prognostic classification model development. (bvsalud.org)

The correlation coefficient is calculated between every pair of genes in every dataset, then the number of datasets in which the pair of genes has a significant correlation with one another is determined. (yeastgenome.org)

Expression microarrays have been widely used to study metastasis in various types of cancer. (nih.gov)
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)
Microarrays are a significant advance because of their small size and are therefore useful when one wants to survey a large number of genes quickly or when the study sample is small. (medscape.com)

For example, studies suggest that ccRCC is closely associated with tumor suppressor von-Hippel Lindau ( VHL ) gene mutations that lead to stabilization of hypoxia inducible factors (HIF-1 α and HIF-2 α , also known as HIF1A and EPAS1) in both sporadic and familial forms [ 5 , 6 ]. (hindawi.com)
Scope includes mutations and abnormal protein expression. (cancerindex.org)
Tobacco smoking is linked to "stop-gain mutations" (SGMs) that interfere with the formation of tumor suppressor genes, which help keep abnormal cells in check, new research suggests . (medscape.com)

The TCGA-CRC and GSE50760 datasets were pre-processed and subjected to feature selection using the LASSO method in combination with five ML algorithms: Adaboost, Random Forest (RF), Logistic Regression (LR), Gaussian Naive Bayes (GNB), and Support Vector Machine (SVM). (bvsalud.org)

A total of 470 DEGs comprising 394 upregulated and 76 downregulated genes were found in pulpitis tissue. (researchsquare.com)
Applications of a rat multiple tissue gene expression data set. (novartis.com)
Tissue localization of gene expression gives some information about the potential role of a gene in physiology. (novartis.com)
Various examples of the utility of multiple tissue gene expression data sets are illustrated here. (novartis.com)
First, we highlight their use in finding genes that might play an important role in a particular tissue on the basis of exclusive expression in that tissue or coexpression with a gene or genes with known function. (novartis.com)
All of these applications of multiple tissue gene expression data sets will play a role in functionally annotating the rat genome. (novartis.com)
Here, we introduce a method that improves dose prediction by integrating tissue-specific gene expression. (biomedcentral.com)
We build gene-tissue signatures associated with warfarin dose in a cohort-specific manner and identify a signature of 11 gene-tissue pairs that significantly augments the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. (biomedcentral.com)

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)

The signature of our top screening hits is significantly correlated with gene expression data from clinical melanoma samples. (cdc.gov)
When comparing differential expression (DE) genes in the autopsy samples of men and women who had had MDD, 633 of 706 transcripts were found in those from men only, and 809 of 882 transcripts were found in those from women only. (medscape.com)
Breast cancer samples with higher APOBEC3A expression were found to have significantly more APOBEC-driven SGMs compared with cancers that had lower expression. (medscape.com)

Publicly available datasets were used for replication. (frontiersin.org)
We identified 18 publicly available gene expression datasets in the Oncomine database comparing distant metastases to primary tumors in various solid tumors which met our eligibility criteria. (nih.gov)
Publicly accessible databases now store nearly 1 million gene-expression datasets, giving researchers a robust resource for discovery. (the-scientist.com)

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)

Disrupted protein interactions identify gene sets involved in risk for ASD. (springer.com)
The study aimed to identify gene signatures for the early detection of CRC using machine learning (ML) algorithms utilizing gene expression data. (bvsalud.org)

With the sequencing and assembly of the rat genome comes the difficult task of assigning functions to genes. (novartis.com)

These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)

Sampling event dataset https://doi.org/10.15468/mb6gst accessed via GBIF.org on 2023-12-01. (gbif.org)

It is applicable to gene expression, DNA methylation, and histone modification etc. (bioconductor.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)

With considerable accumulation of RNA-Seq transcriptome data, we have extended our understanding about protein-coding gene transcript compositions. (nature.com)
Protein-coding transcripts or genes do occupy much higher expression fraction in transcriptome data. (nature.com)
One major difficulty confronted is complex alternatively spliced transcript isoforms in human protein-coding genes. (nature.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)
Next-generation sequencing has not been applied to protein-protein interactome network mapping so far because the association between the members of each interacting pair would not be maintained in en masse sequencing. (nature.com)
Mapping genetic variation to genes improves power and allows the effects of both protein-coding variation as well as variation in expression to be combined into "gene level" effects. (biomedcentral.com)
This method is based on evolutionary algorithm (EA), which effectively fuses protein topology and gene expression data. (biomedcentral.com)
Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division. (karger.com)
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)
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)

The differential expression of IRF4 and IRGs observed in SLE and RA can delineate gene expression signatures associated with clinical features and treatment outcomes. (frontiersin.org)
NEW YORK (GenomeWeb) - The organizers of the Systems Biology Verification: Industrial Methodology for Process Verification in Research (SBV IMPROVER) challenges have begun accepting submissions for a new systems toxicology challenge launched last week which focuses on identifying blood gene expression signatures that could serve as markers of smoking exposure. (genomeweb.com)
It features two sub-challenges: For the first, participants will be expected to derive models that can predict gene signatures for smoking exposure using human whole blood gene expression data. (genomeweb.com)
In the second sub-challenge, participants will also have access to blood gene expression data from mice and will attempt to find species-independent gene signatures that can predict smoking exposure. (genomeweb.com)
CA2, CA7, and ITM2C can serve as gene signatures for the early detection of CRC and may provide valuable information for prognostic and therapeutic decision making. (bvsalud.org)

Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. (cdc.gov)

This approach, as well as the gene signature identified, provides important insights to the common metastatic process and a foundation for future discoveries that could have broad application, such as drug discovery, metastasis prediction, and mechanistic studies. (nih.gov)
Our results demonstrate that imputed expression can improve dose prediction and bridge population-specific compositions. (biomedcentral.com)
In this work, we evaluate the degree to which estimation of baseline gene expression can improve prediction of drug response. (biomedcentral.com)

Genes are also indicated on the heatmap in d . (jneurosci.org)
a , Differential expression of potassium channel genes, depicted as a heatmap of z -score normalized RPKM gene expression values. (jneurosci.org)
Calculate differentially expressed genes and generate a heatmap from the selection you made. (lu.se)

Anatomy15

Organisms11

Diseases4

Chemicals and Drugs46

Analytical, Diagnostic and Therapeutic Techniques and Equipment51

Phenomena and Processes100

Disciplines and Occupations11

Humanities1

Information Science38

Health Care14

Omnibus8

Pathways24

Microarray datasets2

Proteins9

MRNA7

Profiles14

Genomic8

Methods4

Variants3

Genotype-Tissue Expression1

Pathway7

Target genes3

Candidate genes2

Biological6

Enrichment3

Analyses3

20191

Patterns11

Regulate gene expression1

Phenotypes2

Analyze microarray1

Identification8

Common genes1

Ontology2

Analysis26

Experimental3

Correlates2

Tumor genes1

Tissues5

Thousands of genes1

Resistance Genes1

Scientists4

Significantly enriched1

Confirmed in publicly1

Significant genes1

Correlation1

Microarrays3

Mutations3

TCGA1

Tissue8

Putative1

Samples3

Publicly3

High-throughput1

Identify gene2

Genome1

Modulate1

20231

Methylation1

DEGs1

Protein12

Signatures5

Robust1

Prediction3

Heatmap3