Gene expression quantitative trait loci. Medical search. Frequent questions

To test this hypothesis, tumor targeted sequencing data from 12,413 patients across 11 cancer types in the Dana-Farber Profile cohort were integrated with germline cancer gene expression quantitative trait loci (eQTL) from the Genotype-Tissue Expression Project. (nih.gov)
GLI2, WRN, and CBFB eQTL were associated with global tumor mutational burden of cancer genes in ovarian cancer, glioma, and esophagogastric carcinoma, respectively. (nih.gov)
An EPHA5 eQTL was associated with mutations in cancer genes specific to colorectal cancer, and eQTL related to expression of APC, WRN, GLI1, FANCA, and TP53 were associated with mutations in genes specific to endometrial cancer. (nih.gov)
The only considerable difference is that eQTL studies can involve a million or more expression microtraits. (wikipedia.org)
Standard gene mapping software packages can be used, although it is often faster to use custom code such as QTL Reaper or the web-based eQTL mapping system GeneNetwork. (wikipedia.org)
GeneNetwork hosts many large eQTL mapping data sets and provide access to fast algorithms to map single loci and epistatic interactions. (wikipedia.org)
Heterogeneity of expression quantitative trait locus (eQTL) effects have been shown across gene expression processes. (biomedcentral.com)
Genome-wide eQTL analyses with transcriptome-wide gene expression data revealed 20 cis-acting eQTLs associated simultaneously with mRNA expression, ribosome occupancy, and protein abundance. (biomedcentral.com)
A 97 kb-long eQTL signal for mitochondrial ribosomal protein L43 ( MRPL43 ) covered the gene, showing a heterogeneous effect size on gene products across expression stages. (biomedcentral.com)
One allele of the eQTL was associated with increased mRNA expression and ribosome occupancy but decreased protein abundance. (biomedcentral.com)
Expression quantitative trait loci (eQTL) studies in the past decade have demonstrated that gene transcript levels in a cell are frequently associated with nearby genetic variants ( cis -eQTLs), which in turn are enriched for single-nucleotide polymorphisms (SNPs) associated with disease 1 , 2 . (nature.com)
Using a mouse (Mus musculus) model of asthma applied to the Collaborative Cross population, we previously identified a lung gene expression quantitative trait locus (eQTL) for Zinc finger protein 30 (Zfp30) that was also a QTL for neutrophil recruitment and the hallmark neutrophil chemokine CXCL1. (nih.gov)
To search for the genetic variants regulating gene expression in the retina, they used expression quantitative trait loci (eQTL) analysis. (nih.gov)
We have integrated inbred mouse and cell-based models with haplotype association mapping (genetic), global gene expression analyses (genomic), and expression quantitative trait locus mapping (eQTL or genetical genomics) to identify candidate susceptibility genes and associated gene networks. (nih.gov)
Mapping variation in Hspa5 mRNA expression levels in the retina revealed a statistically significant trans -acting expression QTL (eQTL) on Chromosome 2 (Chr 2) and a suggestive locus on Chr 15. (molvis.org)
Gene expression quantitative trait loci (eQTL) are a useful tool for identifying single nucleotide polymorphisms (SNPs) associated with genetic diseases. (nih.gov)
Recent enrichment analyses suggest that there may be true risk variants for bipolar disorder in the expression quantitative trait loci (eQTL) in the brain. (johnshopkins.edu)
Method To detect single nucleotide polymorphisms (SNPs) that influence expression levels of genes associated with bipolar disorder, we jointly analysed data from a bipolar disorder GWAS (7481 cases and 9250 controls) and a genome-wide brain (cortical) eQTL (193 healthy controls) using a Bayesian statistical method, with independent follow-up replications. (johnshopkins.edu)
Here we characterize expression and chromatin state dynamics across three tissues-liver, lung, and kidney-in 47 strains of the Collaborative Cross (CC) mouse population, examining the regulation of these dynamics by expression quantitative trait loci (eQTL) and chromatin QTL (cQTL). (duke.edu)
Leveraging overlapping measurements of gene expression and chromatin accessibility on the same mice from multiple tissues, we used mediation analysis to identify chromatin and gene expression intermediates of eQTL effects. (duke.edu)

Heritable differences in transcribed RNA levels can be mapped as quantitative trait loci (QTLs). (nih.gov)
We have tested heritability-weighted averages to define expression of a transcript and found that these allow detection of more QTLs than previously described methods. (nih.gov)
These have been named expression QTLs (eQTLs). (wikipedia.org)
Many quantitative trait loci (QTLs) have been identified from genome-wide association studies (GWAS) for complex phenotypes over the last decade, but the understanding of their underlying functions is mostly vague [ 1 ]. (biomedcentral.com)
The genetics of gene expression is critical in understanding gene regulation with the QTLs and dissecting the genetic basis of complex phenotypes. (biomedcentral.com)
The papers describe several other types of analyses as well, including variants that alter the length of proteins and those that affect how genes are spliced (splicing QTLs, or sQTLs). (nih.gov)
3. Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. (nih.gov)
To address this gap, Cruchaga and his colleagues compared the overlap between gene expression QTLs (eQTLs) and pQTLs. (genomeweb.com)
What we found is that a lot of the protein QTLs are not expression QTLs [and] are not splicing QTLs," Cruchaga said. (genomeweb.com)
Beyond discovering the small overlap between eQTLs and pQTLs, Seyfried said that one of Cruchaga's key findings is that the majority of cis-pQTLs (genetic variations that act on local genes) are shared across tissues whereas trans-QTLs (those acting on distant genes and genes found on different chromosomes) appear more likely tissue-specific. (genomeweb.com)
Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis -meQTLs (e.g. through disruption of transcription factor binding sites for CTCF and SMC3) and trans -meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). (biomedcentral.com)
Qtlizer annotates lists of common small variants (mainly SNPs) and genes in humans with associated changes in gene expression using the most comprehensive database of published quantitative trait loci (QTLs). (bioconductor.org)
We mapped genomic regions of Quantitative Trait Loci (QTLs) and Expression Quantitative Trait Loci (eQTLs) associated with resistance to P. parasitica in the linkage groups (LGs) of the previously constructed maps of C. sunki and P. trifoliata . (biomedcentral.com)
Though not necessarily genes themselves, QTLs are stretches of DNA that are closely linked to the genes that underlie the trait in question. (dadamo.com)
Typically, QTLs underlie continuous traits (those traits that vary continuously - the trait could have any value within a range - e.g., height) as opposed to discrete traits (traits that have two or several character values - e.g., eye colour or smooth vs. wrinkled peas used by Mendel in his experiments). (dadamo.com)
Consequently, many QTLs are associated with a single trait - these QTLs are often found on different chromosomes. (dadamo.com)
Knowing the number of QTLs that explains variation in the phenotypic trait tells us about the genetic architecture of a trait. (dadamo.com)
Another use of QTLs is to identify candidate genes underlying a trait. (dadamo.com)
Such expression QTLs (e-QTLs) describe cis- and trans-controlling elements for the expression of often disease-associated genes. (dadamo.com)
QTLs identify a particular region of the genome as containing a gene that is associated with the trait being assayed or measured. (dadamo.com)
For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. (bvsalud.org)

Expression quantitative trait loci (eQTLs) are genomic loci that explain variation in expression levels of mRNAs. (wikipedia.org)
Chromosomal loci that explain variance in expression traits are called eQTLs. (wikipedia.org)
eQTLs located near the gene-of-origin (gene which produces the transcript or protein) are referred to as local eQTLs or cis-eQTLs. (wikipedia.org)
By contrast, those located distant from their gene of origin, often on different chromosomes, are referred to as distant eQTLs or trans-eQTLs. (wikipedia.org)
eQTLs may act in cis (locally) or trans (at a distance) to a gene. (wikipedia.org)
The combination of whole-genome genetic association studies and the measurement of global gene expression allows the systematic identification of eQTLs. (wikipedia.org)
Mapping eQTLs is done using standard QTL mapping methods that test the linkage between variation in expression and genetic polymorphisms. (wikipedia.org)
This is especially the case for trans eQTLs that do not benefit from the strong prior probability that relevant variants are in the immediate vicinity of the parent gene. (wikipedia.org)
These findings suggest that multiple functional variants in a linkage exert their regulatory functions at different points in the gene expression process, producing a complexity of single eQTLs. (biomedcentral.com)
A variety of genome-wide identifications of eQTLs have been provided by layers of gene regulation. (biomedcentral.com)
The detection of eQTLs spanning long distances ( trans -eQTLs) has been challenging, particularly due to the multiple testing burden that occurs when genome-wide sets of variants are compared with genome-wide sets of genes. (nature.com)
They furthermore reduced the number of variants to test for trans -eQTLs to 4,542 SNPs that have been implicated in complex traits by genome-wide association studies. (nature.com)
This allowed the detection and replication of trans -eQTLs for 233 disease-associated SNPs (at 103 independent loci), and provided insight into the pathogenesis of disease for selected variants identified in their screen. (nature.com)
This approach can reveal variants that affect gene activity, called expression quantitative trait loci (eQTLs). (nih.gov)
For example, eQTLs with the greatest effects on 2 genes associated with blood pressure had their strongest effects in the tibial artery. (nih.gov)
We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. (nih.gov)
We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. (nih.gov)
Similar to expression (eQTLs), more cis than trans regulation has been identified[ 5 - 7 ] but peak enrichment for mQTLs is located in much closer proximity to transcription start sites than that of eQTLs[ 6 ]. (biomedcentral.com)
After an initial evaluation of 930 tumor samples, follow-up testing showed that nearly every tumor cell presented with at least one non-coding mutation, and that expression quantitative trait loci (eQTLs) were disrupted by non-encoding mutations in 88 percent of cases. (drugdiscoverynews.com)

We hypothesized that germline variants can influence somatic mutations in a nearby cancer gene ("local impact") or a set of recurrently mutated cancer genes across the genome ("global impact") through their regulatory effect on gene expression. (nih.gov)
Variants that upregulate ATM expression were associated with a decreased risk of somatic ATM mutations across 8 cancer types. (nih.gov)
As is true in all QTL mapping studies, the final steps in defining DNA variants that cause variation in traits are usually difficult and require a second round of experimentation. (wikipedia.org)
This study aims to examine fluctuations in differential gene expression by alleles of sequence variants across expression processes. (biomedcentral.com)
Individuals with the TGG haplotype at these three variants had higher levels of mRNA expression and ribosome occupancy than individuals with the GCA haplotype but lower protein levels, producing the flipped effect throughout the expression process. (biomedcentral.com)
In parallel, mechanistic links between the disease-associated variants and the biology of the disease governed by local gene expression alterations are emerging 3 . (nature.com)
An alternate approach to mapping regulatory relationships between genetic variants and distal genes is by correlating genetic variants with genome-wide epigenomic profiles. (nature.com)
The variants that have been linked to human health conditions often alter how genes are expressed-when and where they're turned on and off. (nih.gov)
To help researchers gain deeper insights into how genetic variants affect gene activity and disease susceptibility, NIH launched an effort in 2010 to create a data resource and tissue bank. (nih.gov)
Sophisticated software allowed them to compare genetic variants with the expression of different genes across the different tissues. (nih.gov)
GTEx was designed to sample as many tissues as possible from a large number of individuals in order to understand the causal effects of genes and variants, and which tissues contribute to predisposition to disease," says Dr. Emmanouil Dermitzakis at the University of Geneva Faculty of Medicine, Switzerland, a coauthor of the main Science paper. (nih.gov)
1. Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. (nih.gov)
2. A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits. (nih.gov)
10. Collapsed methylation quantitative trait loci analysis for low frequency and rare variants. (nih.gov)
Previously, Swaroop and colleagues had compared populations of people with and without AMD and identified 34 small genomic regions -called loci-and 52 genetic variants within these loci that were significantly associated with AMD. (nih.gov)
The researchers explored whether the variants might regulate AMD-relevant genes, possibly at promoters, which are sequences within DNA that turn genes on, or enhancers, which increase the activity of promoters. (nih.gov)
If the variants did indeed regulate gene expression, a key question remained: what were the genes that the variants were regulating? (nih.gov)
Computational methods allowed the researchers to detect patterns between the genes expressed in the retina and a pool of more than 9 million previously identified genetic variants. (nih.gov)
Specifically, they looked for variants with a high probability of being responsible for variations in gene expression among people with and without AMD. (nih.gov)
The aim of our study was to evaluate the association between genetic variants in IL17 pathway genes with asthma and atopy markers. (springer.com)
The others genetic variants in the IL 17 pathways genes were associated with both protection and risk for asthma development as well as with IgE levels. (springer.com)
The genetic variants in IL-17-related genes are associated with the atopic asthma phenotype and IgE production. (springer.com)
While these studies have uncovered numerous biomarkers of disease and shed light on disease mechanisms, they tend to fall short of identifying the functional variants and genes that drive GWAS signals. (genomeweb.com)
DNA sequence variants in known breast cancer susceptibility genes (eg. (otago.ac.nz)
The stepwise refinement of candidate genes was based on expression QTL mapping, gene expression correlation analyses (direct and partial), and analysis of regional sequence variants. (molvis.org)
2) Can we map causal relations between gene variants and behavioral differences? (nih.gov)
A comprehensive molecular study identified 12 complementation groups with 56 novel FANC gene variants in Indian Fanconi anemia subjects. (cdc.gov)
To infer molecular pathways that regulate expression variants, we ranked TReQTLs by connectivity within the structure of biological process subtrees that TReQTL SNPs, TRs and targets represent. (nih.gov)
The structure of the subtree and a gene interaction network of the Foxp3 X-linked breast cancer suppressor TReQTL in CEU revealed that tumor necrosis factor, NF-kappaB and variants in G-protein coupled receptors signaling may play a role as communicators in the transfactor's functional regulation. (nih.gov)
they also highlight the informative value of integrating functional annotation of genetic variants for gene expression in advancing our understanding of the biological basis underlying complex disorders, such as bipolar disorder. (johnshopkins.edu)
We find strong support for the classical model of genetic variants regulating methylation, which in turn regulates gene expression. (biomedcentral.com)
Attempts to identify three-way associations between genetic variants, expression and methylation on a genome-wide scale in four different brain regions did not identify co-regulation of methylation and expression by the same genetic variants[ 6 ], while a study of cerebellar samples did identify three-way associations for a number of genes[ 7 ]. (biomedcentral.com)
In lymphoblastoid cell lines of 77 individuals of the Yoruba Hapmap population, co-regulation of expression and methylation levels by the same genetic variants was also found, suggesting a shared mechanism, whereby a genetic variant influences methylation, which in turn influences expression levels[ 5 ]. (biomedcentral.com)
To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. (bvsalud.org)
A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis. (cdc.gov)

Several genes have been associated with distinct asthma phenotypes. (springer.com)
Subobjective 1c: Identify candidate genes for traits by their proximity to QTL, by homology to genes characterized in other systems, and by expression studies on plants with contrasting phenotypes. (usda.gov)
Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1520 co-localisations across 1325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). (biomedcentral.com)
Owing to reducing the interference of complex genetic backgrounds in populations, CSSLs are appropriate for fine mapping significant genes that regulate complex and variable phenotypes or traits, particularly quantitative traits with relatively small genetic effects [ 3 ], which have been widely applied to quantitative trait locus (QTL) mapping for yield, quality, stress tolerance, and disease resistance in commercial crops [ 4 - 8 ]. (techscience.com)
QTL mapping is the statistical study of the alleles which occur in a locus and the phenotypes (physical forms or traits) that they produce. (dadamo.com)

8. DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs. (nih.gov)
Most studies typically associate genetic variation at single nucleotide polymorphisms (SNPs), or methylation quantitative trait loci (meQTLs), to DNA methylation levels at a specific CpG. (biomedcentral.com)
We used a multivariate regression with the gene expression of known targets of TRs as the response and individual SNPs as predictors to identify TReQTLs in European (CEU) and African (YRI) populations revealing 234 and 154 SNPs as TReQTLs, respectively. (nih.gov)

Many expression QTL studies were performed in plants and animals, including humans, non-human primates and mice. (wikipedia.org)

Genes may be on the same or different chromosomes and each gene may have two or more alleles.Once a region of DNA is identified as contributing to a phenotype, it can be sequenced. (dadamo.com)
Statistical analysis is required to demonstrate that different genes interact with one another and to determine whether they produce a significant effect on the phenotype. (dadamo.com)
For example, they may be interested in knowing whether a phenotype is shaped by many independent loci, or by a few loci, and do those loci interact. (dadamo.com)
In general two approaches can be taken: i) candidate gene studies have mostly used transgenic models to investigate a role of a specific gene in the regulation of anxiety, and ii) genome-wide approaches do not make any prior assumptions regarding which genes contribute to the phenotype. (biomedcentral.com)

This FOA solicits applications to develop innovative statistical methods to detect the influence of genetic variation on tissue-specific gene expression and regulation. (nih.gov)
By assaying gene expression and genetic variation simultaneously on a genome-wide basis in a large number of individuals, statistical genetic methods can be used to map the genetic factors that underpin individual differences in quantitative levels of expression of many thousands of transcripts. (wikipedia.org)
One form of epigenetic variation is methylation at CpG sites, which can be measured as methylation quantitative trait loci (meQTL). (nature.com)
Second, using site-directed mutagenesis followed by reporter gene assays, we identified a single variant, rs51434084, which explained the majority of variation in expression between two out of three haplotype groups. (nih.gov)
Importantly, the ability to define how genetic variation affects gene expression opens up entirely new directions for looking at the biology of the eye," Swaroop said. (nih.gov)
The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. (biomedcentral.com)
Although we did not identify specific loci showing robust differences in neonatal DNA methylation associated with later ASD, there was a significant association between increased polygenic burden for autism and methylomic variation at specific loci. (biomedcentral.com)
Furthermore, common variation in many genes contributes to risk of sporadic PD. (nih.gov)
Moreover, very little is known about how inter-individual genetic variation contributes to protein expression patterns. (rti.org)
To begin to address this, we describe elements of technical and biological variation contributing to expression of 544 proteins in a population of 24 individual human lymphoblastoid cell lines (LCLs) that have been extensively genotyped as part of the International HapMap Project. (rti.org)
Using the publicly available genotypes for these LCLs, we applied a genetic association approach to identify quantitative trait loci associated with protein expression variation (peQTL). (rti.org)
50% of the expression variation. (rti.org)
The genetic variation associated with protein expression levels were located in cis with the gene coding for the protein's transcript for 19 of these protein forms. (rti.org)
Some useful variation might exist due to random mutations, but nearly all such cases would correspond to degradations of genes (i.e., the loss of information) or to trivial modifications that could never accumulate to significantly alter any trait ( here , here ). (evolutionnews.org)
there is an emerging view that additive genetic variation accounts for a relatively small percentage of phenotypic variation and rather it's the context in which traits develop that determines their final form (Hendrikse et al. (evolutionnews.org)
The analysis of gene expression profile demonstrated a great variation of responses regarding the activation of plant defense pathways, indicating that citrandarins have several defense strategies to control oomycete infection. (biomedcentral.com)
However, recent studies suggest that the relationship between genetic variation, DNA methylation and expression is more complex. (biomedcentral.com)
A structural equation model based analysis found strong support in particular for a traditional causal model in which gene expression is regulated by genetic variation via DNA methylation instead of gene expression affecting DNA methylation levels. (biomedcentral.com)
Local ( cis ) and distal ( trans ) associations of genetic variation with gene expression levels have been observed. (biomedcentral.com)
We found that latitude-related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. (bvsalud.org)
This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by-environment interaction that underlies variation in the mean and plasticity of maize complex traits. (bvsalud.org)
Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a system-wide scale. (bvsalud.org)
Of interest, combining genetic variation (i.e. inter-individual changes in the DNA) with gene expression, we showed that besides immune cells in the blood, other organs such as the liver and the brain are involved in causing the disease. (foreum.org)

Using GWAS summary statistics from the Population Architecture using Genomics and Epidemiology (PAGE) study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we applied S-PrediXcan to perform PWAS for 28 complex traits. (plos.org)
The QTL mapping approach identified a list of prime candidate genes for further validation using functional genomics or forward genetics approaches. (biomedcentral.com)

Differential Regulation of Zfp30 Expression in Murine Airway Epithelia Through Altered Binding of ZFP148 to rs51434084. (nih.gov)
The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. (nih.gov)
Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. (frontiersin.org)
instead they are hypothesized to influence gene regulation. (biomedcentral.com)
Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. (biomedcentral.com)
In total, 5,673 differentially expressed genes (DEGs) were identified from multi-sample comparisons, which were mainly involved in the oxidation-reduction process, protein phosphorylation, regulation of transcription, DNA template, and carbohydrate metabolic process. (techscience.com)
It has been common to consider the existence of hot spots as evidence for master regulation of gene expression. (columbia.edu)
The predominant model for regulation of gene expression through DNA methylation is an inverse association in which increased methylation results in decreased gene expression levels. (biomedcentral.com)
Scholars@Duke publication: Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. (duke.edu)
Based on QTL and mediation analyses over multiple tissues, we propose a causal model for the distal genetic regulation of Akr1e1, a gene involved in glycogen metabolism, through the zinc finger transcription factor Zfp985 and chromatin intermediates. (duke.edu)
Continued studies focused on genes showing minimal changes in the TMA-induced model but with clear up-regulation in the ovalbumin model. (cdc.gov)

In addition, we performed DNA methylation quantitative trait loci (mQTL) mapping to prioritize target genes from ASD GWAS findings. (biomedcentral.com)

In the past, genome-wide association studies (GWAS) have identified an important number of risk loci associated with AD pathology 3 , but a causal relationship remains difficult to establish. (nature.com)
13. Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue. (nih.gov)
The authors used 3 complementary, objective methods to help determine the underlying causal gene at each of the candidate loci. (medscape.com)
However, as noted in the editorial accompanying the manuscript, [ 2 ] "in the end the authors used the old-fashioned approach of placing loci (and predicted causal genes) into. (medscape.com)

We then performed genome-wide mapping of the IL1beta results and found a significant marker (quantitative trait locus) on distal chromosome 7. (cdc.gov)
Searching that area on Chromosome for possible candidate genes, we identified Spondin 1 as candidate. (cdc.gov)
Chromosome segment substitution lines (CSSLs) have been introduced in cotton breeding to take full advantages of superior fiber quality and high yield from Sea Island and Upland cotton, respectively, which serve as ideal materials for elucidating the genetic mechanism of complex quantitative traits. (techscience.com)
Our results provide novel insights into the mechanism underlying fiber formation and lay a solid foundation for further high-efficiency determination of candidate genes by combining RNA-seq data and pivotal chromosome regions. (techscience.com)
Hence, it may be useful to combine the superior traits of Upland and Sea Island cotton species to generate high-yield and fine fiber-quality varieties using chromosome segment substitution lines (CSSLs). (techscience.com)
Pathogen genetics identifies avirulence/virulence loci associated with barley chromosome 6H resistance in the Pyrenophora teres f. teres - barley interaction. (usda.gov)
A candidate gene is a gene, located in a chromosome region suspected of being involved in the expression of a trait such as a disease, whose protein product suggests that it could be the gene in question. (dadamo.com)
Transcription activity 'hot spots', defined as chromosome regions that contain more expression quantitative trait loci than would have been expected by chance, have been frequently detected both in humans and in model organisms. (columbia.edu)

A recent simulation study using real human gene expression data but simulated random single-nucleotide polymorphism genotypes showed patterns of clustering of expression quantitative trait loci that resemble those in actual studies [Perez-Enciso: Genetics 2004, 166: 547-554. (columbia.edu)
Genetics offer an ideal route to the molecular background of anxiety as any identified genes can directly be linked to their function within the cell and the neural circuits. (biomedcentral.com)
Both genetics and environmental factors influence the expression of asthma, and not all asthma is the result of a specific immune response to allergen. (cdc.gov)

Follow-up studies across multiple independent samples confirmed the association of the risk SNP (rs6088662) with gene expression and bipolar disorder susceptibility (P = 3.5461078). (johnshopkins.edu)

DNA methylation map of mouse and human brain identifies target genes in Alzheimer's disease. (nature.com)
Integration of genome-wide association study and expression quantitative trait loci data identifies AIM2 as a risk gene of periodontitis. (cdc.gov)

Although cells contain a myriad of biomolecules that can potentially be assayed across large numbers of genetically characterized samples, analyses of nucleic elements such as transcript expression and CpG methylation are ideally suited for genome-wide comparisons with currently available technologies. (nature.com)
Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. (frontiersin.org)
Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages. (frontiersin.org)
In silico analyses were performed using rSNPbase, RegulomeDB, and Gtex portal for in silico gene expression. (springer.com)
In a recent development, classical QTL analyses are combined with gene expression profiling i.e. by DNA microarrays. (dadamo.com)
In this study, to assess the credibility of transcription activity hot spots, we conducted genetic analyses on gene expressions provided by Genetic Analysis Workshop 15 Problem 1. (columbia.edu)
Following these analyses, we mapped a list of 15 genes that can predict major organ involvement (kidney, brain, etc.) in a given SLE patient, based upon the pattern of gene expression of these genes. (foreum.org)

The third approach looked for co-expression of clusters of genes by assessing suspected candidate genes relative to known susceptibility loci. (medscape.com)
Optimization of highly efficient exogenous-DNA-free Cas9-ribonucleoprotein mediated gene editing in disease susceptibility loci in wheat (Triticum aestivum L.). Frontiers in Plant Science. (usda.gov)

6. Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes. (nih.gov)
With the arrival of high-throughput DNA methylation assays, methylation quantitative trait loci (mQTLs) can now be studied genome-wide in any tissue or cell type of interest. (biomedcentral.com)

Of them, 11 genes were putative wheat orthologs of known Arabidopsis and rice genes related to Zn/Fe homeostasis. (cgiar.org)
If the genome is not available, it may be an option to sequence the identified region and determine the putative functions of genes by their similarity to genes with known function, usually in other genomes. (dadamo.com)
A list of candidate genes with related putative function, location close to QTL maxima and with the highest expression level in the phloem, xylem and cambium was identified. (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)

Improved high-throughput technology allows similar interrogation of the genetically regulated proteome for understanding complex trait mechanisms. (plos.org)

We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2358 blood samples from three UK cohorts. (biomedcentral.com)

Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box ( DAM ) genes (DAM4 , DAM5 , and DAM6 ). (frontiersin.org)

9. Genome-wide identification of cis DNA methylation quantitative trait loci in three Southeast Asian Populations. (nih.gov)
To complement human genetic studies several groups have used mouse models of anxiety-like behavior for identification of genes and biological pathways that regulate anxiety. (biomedcentral.com)
In this review, we will concentrate on genome-wide approaches in mice, which have resulted in the identification of genes regulating anxiety. (biomedcentral.com)
Different statistical methods with varying selection criteria resulted in identification of similar candidate genes. (cdc.gov)

Statistical, graphical, and bioinformatic methods are used to evaluate positional candidate genes and entire systems of interactions. (wikipedia.org)
In this study, we used systems genetic methods, statistical modeling, and immunostaining to identify and analyze candidate genes that modulate Hspa5 expression in the retina. (molvis.org)
The aim is to find a marker that is significantly more likely to co-occur with the trait than expected by chance, that is, a marker that has a statistical association with the trait. (dadamo.com)
Another interest of statistical geneticists using QTL mapping is to determine the complexity of the genetic architecture underlying a phenotypic trait. (dadamo.com)

The information of the phenotypic and gene expression data made possible to detect genomic regions associated with resistance. (biomedcentral.com)
Moreover, a single phenotypic trait is usually determined by many genes. (dadamo.com)
When a QTL is found, it is often not the actual gene underlying the phenotypic trait, but rather a region of DNA that is closely linked with the gene. (dadamo.com)
Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. (bvsalud.org)

In reporter gene assays in vitro, these haplotypes recapitulated the three previously identified in vivo expression patterns. (nih.gov)
They were able to cluster genes into "modules" with coordinated expression patterns in different tissues. (nih.gov)
A companion study in Science examined patterns in gene activity across nearly 1,500 GTEx tissue samples. (nih.gov)
We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. (frontiersin.org)
Population-based variability in protein expression patterns, especially in humans, is often observed but poorly understood. (rti.org)
Eight temporal expression patterns were monitored on the DEGs of different lines, of which the significantly enriched profile revealed higher similarities between two superior CSSLs or the ordinary CSSL and CCRI45 with respect to fiber performance. (techscience.com)
These lines differ very widely in patterns of gene and protein expression in the brain and in patterns of behavior. (nih.gov)

Carlos Cruchaga, a professor of psychiatry at Washington University who studies the biology of neurodegenerative disease, recently described how he has used SomaLogic's SomaScan technology to uncover approximately 2,300 protein quantitative trait loci (pQTLs) and 400 proteins implicated in Alzheimer's disease in samples of cerebrospinal fluid (CSF), brain tissue, and plasma. (genomeweb.com)
There are several other genes encoding proteins that act in the mismatch repair pathway, but evidence for the involvement of these and other genes in endometrial cancer susceptibility is currently limited. (otago.ac.nz)
We determined that expression levels of 10% of the proteins were tightly correlated to cell-doubling rates. (rti.org)
We have used RNA-Seq and genome-wide association studies to uncover genes and their products (RNA or proteins) that can be used as markers to predict patients more likely to develop severe lupus and respond to therapy. (foreum.org)
We have used RNA Sequencing to uncover genes and their products (RNA or proteins) that can be used as markers to predict patients who may be more susceptible to certain serious manifestations of lupus as well as to interrogate the cells in the bone marrow (stem cells) to identify targets for new therapies. (foreum.org)

An expression quantitative trait is an amount of an mRNA transcript or a protein. (wikipedia.org)

Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. (nih.gov)
The most protein-trait associations were discovered, colocalized, and replicated in large independent GWAS using proteome prediction model training populations with similar ancestries to PAGE. (plos.org)
Tools including in silico haplotyping, collaborative cross and diversity outcross mouse panels, bioinformatic applications, and -omics technologies have enhanced our ability to identify disease genes and pathways to guide translational investigations that apply these discoveries to human populations. (nih.gov)
Objective 1: Deliver enhanced genomic resources for blueberry and cranberry breeding and genetic research including: improved genome assemblies, germplasm genotypes, mapping populations, saturated genetic linkage maps, mapping data for high value quantitative traits, and candidate gene analysis using genetic and bioinformatic approaches. (usda.gov)
Subobjective 1b: Map QTL for cold hardiness, chilling requirement, fruiting season, disease resistances, and fruit quality traits using improved maps and well-characterized bi-parental and association mapping populations. (usda.gov)
Scientists will develop enhanced genomic resources for blueberry and cranberry, including improved genome assemblies, well-saturated genetic linkage maps with anchorage to the genomes, and well-characterized bi-parental and association mapping populations, and identify quantitative trait loci (QTL) for horticulturally significant traits such as cold hardiness, chilling requirement, fruiting season, disease resistances, and fruit quality traits. (usda.gov)
Spectrum of Germline Mutations Within Fanconi Anemia-Associated Genes Across Populations of Varying Ancestry. (cdc.gov)

As a result, the number of known loci of celiac disease susceptibility genes has increased from 14 to 27. (medscape.com)

7. Pathway analysis using information from allele-specific gene methylation in genome-wide association studies for bipolar disorder. (nih.gov)
11. A meta-analysis of gene expression quantitative trait loci in brain. (nih.gov)
14. Methylation quantitative trait locus analysis of osteoarthritis links epigenetics with genetic risk. (nih.gov)
The analysis pointed to target disease genes at six of the 34 AMD loci identified in the earlier research. (nih.gov)
This analysis also suggested as many as 20 additional candidate genes providing insights into the genes and pathways involved in pathobiology of AMD. (nih.gov)
Here we show that GWAS meta-analysis of glucose measurements under nonstandardized conditions (random glucose (RG)) in 476,326 individuals of diverse ancestries and without diabetes enables locus discovery and innovative pathophysiological observations. (imperial.ac.uk)
Sulf2 on Chr 2 was the strongest candidate gene based on partial correlation analysis, Pearson correlation with Hspa5 , expression levels in the retina, a missense variant in exon 14, and its reported function in the extracellular matrix and interphotoreceptor matrix. (molvis.org)
Plasma tumor gene conversions after one cycle abiraterone acetate for metastatic castration-resistant prostate cancer: a biomarker analysis of a multicenter international trial. (cdc.gov)
Additional analysis of TCGA-data was performed to assess the general alteration of DR6 in cancer and influence of IDH-mutation on DR6 expression in gliomas. (cancerindex.org)
A weighted correlation network analysis revealed that i) both transcriptome and methylome are organized in modules, ii) co-expression modules are generally not preserved in the methylation data and vice-versa, and iii) highly significant correlations exist between co-expression and co-methylation modules, suggesting the existence of factors that affect expression and methylation of different modules (i.e., trans effects at the level of modules). (biomedcentral.com)
Our analysis also confirmed the critical role of the immune system (e.g. over-expression of the antiviral interferon-alpha) in the causation of the SLE. (foreum.org)

Combined genetic and genomic approaches have yielded important insight to mechanisms of susceptibility to many complex traits and diseases. (nih.gov)
Systems genetic approaches for examining relationships between gene expression and methylation array data were used to find both negative and positive associations between these levels. (biomedcentral.com)
Here, we integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition. (bvsalud.org)

We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. (nature.com)

Observed epistatic effects have been found beneficial to identify the gene responsible by a cross-validation of genes within the interacting loci with metabolic pathway- and scientific literature databases. (dadamo.com)

In 2007, a genome-wide association study (GWAS) identified 14 genes related to innate and adaptive immunity important to susceptibility to celiac disease. (medscape.com)
[ 1 ] In the current study, a GWAS was performed on 6 times as many samples, using 5 European case-control data sets that consisted of 4533 cases of celiac disease and 10,750 controls, and tested nearly 300,000 genes. (medscape.com)

The second approach used expression quantitative trait locus mapping, which highlights the contribution of alterations that may influence gene expression rather than protein structure and function. (medscape.com)
NEW YORK - Comparisons of gene expression and protein quantitative trait loci reveal post-translational modifications that may drive the occurrence and development of Alzheimer's disease. (genomeweb.com)
We have previously demonstrated that the photoreceptor membrane-associated protein XAP-1 antigen is a product of the HSPA5 gene. (molvis.org)
The protein encoded by this gene is the NADP(+)-dependent isocitrate dehydrogenase found in the mitochondria. (cancerindex.org)
What does this gene/protein do? (cancerindex.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)
Scope includes mutations and abnormal protein expression. (cancerindex.org)

The abundance of a gene transcript is directly modified by polymorphism in regulatory elements. (wikipedia.org)
Gene transcription profiles across tissues are largely defined by the activity of regulatory elements, most of which correspond to regions of accessible chromatin. (duke.edu)

Mutations in the mismatch repair genes MLH1, MSH2, MSH6 and PMS2 are known to confer increased risk in a proportion of endometrial cancer cases. (otago.ac.nz)
A team of researchers at the University of California, San Diego School of Medicine and Moores Cancer Center have broadened that view to include nearly 200 mutations that occur in DNA that do not encode genes, but still demonstrate the ability to change gene expression. (drugdiscoverynews.com)
Most cancer-related mutations occur in regions of the genome outside of genes, but there are so incredibly many of them that it's hard to know which are actually relevant and which are merely noise," said senior author Dr. Trey Ideker, professor at UC San Diego School of Medicine and Moores Cancer Center. (drugdiscoverynews.com)
Studies into inherited breast cancer have shown that PARP inhibitors can be effective in killing the BRCA1 gene, a prime example of both coding and non-coding mutations. (drugdiscoverynews.com)

Feilich noted that changes in traits were highly correlated to optimize hydrodynamics and maneuvering. (evolutionnews.org)
However, hot spots could also simply be due to highly correlated gene expressions or linkage disequilibrium and do not truly represent master regulators. (columbia.edu)
Moreover we show that, although the methylation and expression modules differ, they are highly correlated. (biomedcentral.com)

Several methods, such as quantitative trait locus mapping, gene expression profiling, and proteomics, have been used in various mouse models of anxiety to identify genes that regulate anxiety or play a role in maintaining pathological anxiety. (biomedcentral.com)
We then describe how several genes have been identified through genome-wide methods in mouse models and subsequently investigated in human anxiety disorder samples as candidate genes. (biomedcentral.com)

The first genome-wide study of gene expression was carried out in yeast and published in 2002. (wikipedia.org)
4. Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci. (nih.gov)
We used a systems biology approach that integrates this genome-wide transgenesis with full genome information to advance our understanding of wood formation and how to engineer woody plants to create robust feedstocks that maximize beneficial traits for biofuel and material production. (osti.gov)
As anxiety is an evolutionarily conserved response, mouse models can be used to carry out genome-wide searches for specific genes in a setting that controls for the environmental factors. (biomedcentral.com)
The multi-omics integrative network map illustrates the principles of how molecular networks connect different types of genes and potential pathways to map a genome-wide functional landscape in maize, which should be applicable in a wide range of species. (bvsalud.org)

This map comprises over 2.8 million edges in more than 1,400 functional subnetworks, demonstrating an extensive network divergence of duplicated genes. (bvsalud.org)

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. (nature.com)
The activity of almost 2,000 genes varied with age, including genes in pathways related to neurodegenerative disorders such as Parkinson's disease and Alzheimer's disease. (nih.gov)

This distinguishes expression quantitative traits from most complex traits, which are not the product of the expression of a single gene. (wikipedia.org)
This resource will enable new discoveries of the genetic influences of complex behavioral traits. (nih.gov)
Genetically regulated gene expression has helped elucidate the biological mechanisms underlying complex traits. (plos.org)
NP 301, C1, PS1B] Objective 4: Identify and characterize key pathogens of blueberry and cranberry and the genes that mediate plant-pathogen interactions, including stem blight (blueberry) and key pathogens in the fruit rot complex (cranberry), as well as plant-environment interactions. (usda.gov)
Scientists will also identify key genes in blueberry and cranberry that mediate plant-pathogen interactions, including stem blight (blueberry), key pathogens in the fruit rot complex (cranberry), and plant-environment interactions. (usda.gov)
Our results provide new insights into the complex mechanisms between genetic markers, epigenetic mechanisms and gene expression. (biomedcentral.com)
However, few agronomically important maize genes have been cloned and used for trait improvement, due to its complex genome and genetic architecture. (bvsalud.org)

Based on gene annotations and expression profiles, 28 promising candidate genes were identified for Zn/Fe uptake (8), transport (11), storage (3), and regulations (6). (cgiar.org)
A wheat multidrug and toxic compound extrusion (MATE) transporter TraesCS3A01G499300, the ortholog of rice gene OsPEZ2, was identified as a potential candidate gene. (cgiar.org)
This study has advanced our knowledge of the genetic basis underlying GZnC and GFeC in wheat and provides valuable markers and candidate genes for wheat biofortification. (cgiar.org)
We identified Sulf2 as a candidate gene modulating the Hspa5 expression in the retina. (molvis.org)
In addition, we evaluated the expression of 19 candidate genes involved in citrus defense response 48 h after pathogen infection by quantitative Real-Time PCR (qPCR). (biomedcentral.com)
Candidate genes for bark texture included an ortholog of Arabidopsis ANAC104 (PopNAC128), which plays a role in lignified fiber cell and ray development, as well as Pinin and Fasciclin (PopFLA) genes with a role in cell adhesion, cell shape and migration. (biomedcentral.com)
Array data are intended to provide candidate genes for hypothesis generation and further experimentation. (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)

We are utilising large genetic datasets to identify common and rare genetic changes in these genes that are associated with endometrial cancer risk. (otago.ac.nz)

Applicants are encouraged to take advantage of existing tissue-specific gene expression datasets and/or simulated datasets, but will also be strongly encouraged to utilize GTEx-generated data, if and when it is available. (nih.gov)
Comparison of the data might help in understanding the specific function during each expression stage. (biomedcentral.com)
A new data resource allows scientists to examine how genomic differences affect gene activity in tissues and organs across the body. (nih.gov)
A new data resource will help establish how differences in an individual's genomic makeup can affect gene activity and contribute to disease. (nih.gov)
In addition, integration of this data with earlier AMD studies identified three additional target AMD genes, which had never before been shown to play a role in AMD. (nih.gov)
Based on the intersection between the predicted introgressive genes from RNA-seq data and the published gene information from the G. barbadense genome, 1,535 introgressive genes were identified in three CSSLs. (techscience.com)
In this chapter, we address the following set of related questions: (1) Can we combine massive genomic data sets with large aggregates of precise quantitative data on behavior? (nih.gov)
These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies. (uni-wuerzburg.de)
Comparing quantitative trait loci and gene expression data. (psu.edu)
Organ involvement was predicted with high accuracy (accuracy=0.89, sensitivity=0.89, specificity=0.88 in the validation data) using 25 genes based on the elastic net generalised linear model. (foreum.org)

The Genotype-Tissue Expression (GTEx) project aims to collect tissue samples spanning 54 distinct body sites from 900 deceased donors, including samples from autopsy and organ donations and tissue transplant programs. (nih.gov)

More than 750 genes showed differences in activity between men and women. (nih.gov)
16. Genetic control of individual differences in gene-specific methylation in human brain. (nih.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)

In addition, scientists will carry out gene expression studies to identify the actual genes underlying significant QTL. (usda.gov)
We applied this map to identify factors regulating flowering time and identified 2,651 genes enriched in eight subnetworks. (bvsalud.org)

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. (neurotree.org)

North American Brain Expression Consortium. (nih.gov)
UK Brain Expression Consortium. (nih.gov)
Dillman AA, Majounie E, Ding J, Gibbs JR, Hernandez D, Arepalli S, Traynor BJ, Singleton AB, Galter D, Cookson MR. Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging.Sci Rep. 2017 Dec 4;7(1):16890. (nih.gov)

The use of recombinant inbred lines allows an estimate of the heritability of expression measured by individual probes. (nih.gov)

Quantitative trait locus (QTL) mapping was used to map the genomic region that regulates Hspa5 in the cross between C57BL/6J X DBA/2J mice (BXD) genetic reference panel. (molvis.org)

These sites are relatively rare in the genome but more common at promoter regions of genes, also called CpG islands (CGIs). (biomedcentral.com)
However, negative associations between methylation and expression were found to be enriched particularly in CGIs[ 6 ] and promoter regions[ 5 ]. (biomedcentral.com)
Previous studies identified one non-coding gene, known as TERT, that when mutated was shown to be a tumor promoter by altering DNA replication sequences and allowing tumor cells to become functionally immortal through unregulated division and self-renewal. (drugdiscoverynews.com)
One tumor promoter found in the initial study activated the DAAM1 gene, which then made the tumor cells more aggressive and better able to invade surrounding tissues. (drugdiscoverynews.com)

Fanconi anemia gene-associated germline predisposition in aplastic anemia and hematologic malignancies. (cdc.gov)

Anatomy3

Organisms4

Diseases1

Chemicals and Drugs2

Analytical, Diagnostic and Therapeutic Techniques and Equipment13

Phenomena and Processes28

Disciplines and Occupations3

Technology, Industry, Agriculture2

Information Science4

Health Care4

EQTL20

QTLs21

EQTLs19

Variants35

Phenotypes5

SNPs3

Including humans1

Phenotype4

Variation23

Genomics2

Regulation11

Performed DNA methylation1

Causal4

Chromosome8

Genetics3

Bipolar disorder susceptibility1

Identifies2

Analyses7

Susceptibility loci2

MQTLs2

Putative4

Regulated proteome1

MeQTL1

Differentially expressed genes1

Identification4

Statistical4

Phenotypic4

Patterns7

Proteins5

MRNA1

Populations7

Disease susceptibility1

Analysis11

Approaches3

Haplotype1

Epistatic1

GWAS2

Protein7

Regulatory2

Mutations4

Highly correlated3

Methods2

Genome-wide5

Functional1

Alzheimer's2

Complex7

Candidate8

Endometrial cancer1

Data10

Genotype-Tissue Expression1

Differences3

Identify2

Risk genes1

Brain3

Heritability1

Mice1

Promoter4

Germline1