Genes are clustered. Medical search. Frequent questions

First, genes are clustered into gene groups with a clustering algorithm so that genes belonging to the same cluster have similar expression profile. (mun.ca)
An in-depth analysis can reveal important insights about the performance of the algorithm, the expected quality of the output clusters, and the possibilities for extracting more relevant information out of a particular data set. (ugent.be)
We have extended an existing algorithm for model based clustering of genes to simultaneously cluster genes and conditions, and used 3 large compendia of gene expression data for S. Cerevisiae to analyze its properties. (ugent.be)
The algorithm uses a Bayesian approach and a Gibbs sampling procedure to iteratively update the cluster assignment of each gene and condition. (ugent.be)
Using the $K$-means clustering algorithm we determine the organisation of the solution space for a variety of gene expression datasets using energy landscape theory. (arxiv.org)
In this paper, we propose a novel module detection algorithm based on topology potential and spectral clustering algorithm to detect co-expressed modules in gene co-expression networks. (biomedcentral.com)
Firstly, we used clustering algorithms, Markov cluster algorithm (MCL), Molecular complex detection (MCODE) and Clique percolation method (CPM) to decompose human PPI network into dense clusters as the candidates of disease-related clusters, and then a log likelihood model that integrates multiple biological evidences was proposed to score these dense clusters. (ijbs.com)
Researchers from the Salk Institute for Biological Studies, the University of California, San Diego, and the University of Illinois at Urbana-Champaign present an algorithm called scHiCluster for imputing and clustering Hi-C interaction profiles from single cells. (genomeweb.com)
In this regard, a gene clustering algorithm, termed as robust rough-fuzzy c-means, is proposed judiciously integrating the merits of rough sets and fuzzy sets. (iitj.ac.in)
An efficient method is proposed to select initial prototypes of different gene clusters, which enables the proposed c-means algorithm to converge to an optimum or near optimum solutions and helps to discover coexpressed gene clusters. (iitj.ac.in)
Significance of platelet adhesion-related genes in colon cancer based on non-negative matrix factorization-based clustering algorithm. (bvsalud.org)

Abstract Combinational therapy with small RNA inhibitory agents against multiple viral targets allows efficient inhibition of viral production by controlling gene expression at critical time points. (ca.gov)
abstract = "By culturing microorganisms under standard laboratory conditions, most biosynthetic gene clusters (BGCs) are not expressed, and thus, the products are not produced. (dtu.dk)

The visualization of cluster solutions in gene expression data analysis gives practitioners an understanding of the cluster structure of their data and makes it easier to interpret the cluster results. (uni-muenchen.de)
The number of clusters in gene expression data is for biological reasons rather large. (uni-muenchen.de)
We profile chromatin accessibility and gene expression in Pogz −/− mice and find that POGZ promotes chromatin accessibility of candidate regulatory elements (REs) and the expression of clustered synaptic genes. (biorxiv.org)
We postulate that reduced POGZ dosage disrupts cortical function through alterations in the POGZ-ADNP balance which modifies neuronal gene expression. (biorxiv.org)
Over the last decade, a large variety of clustering algorithms have been developed to detect coregulatory relationships among genes from microarray gene expression data. (ugent.be)
Joshi, A. , Van de Peer, Y. , Michoel, T. (2008) Analysis of a Gibbs sampler method for model based clustering of gene expression data. (ugent.be)
Gene expression profiles are essential in identifying different cancer phenotypes. (arxiv.org)
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)
Interestingly, cells with optimal level of small RNA expression to effectively inhibit viral replication were enriched under the selective pressure of HIV, demonstrating the importance of balancing expression and functionality for successful gene therapy applications. (ca.gov)
To derive a systems view for the regulation of the metabolism when cells adapt to environmental changes, whole genome gene expression profiles can be analysed. (sciweavers.org)
Toxicogenomics tries to understand and predict drug toxicity by studying gene expression. (cam.ac.uk)
The three genes are expressed together in larval stages and adults but show a different pattern of developmental expression from the third instar larval cuticle protein genes. (caltech.edu)
Thus two small gene families can lie adjacent on the chromosome and exhibit different patterns of developmental expression, even though individual genes within a clustered family are coordinately expressed. (caltech.edu)
The single-nucleotide polymorphism rs1582763 modified expression of the MS4A4A and MS4A6A genes in multiple tissues, suggesting that one or both of these genes are important for modulating sTREM2 production. (lu.se)
This study reports a 22-bp nucleotide insertion-deletion (indel) genetic polymorphism that may be causally related to the control of gene expression of the fatty acid desaturases, enzymes that control the biosynthesis of long-chain polyunsaturated fatty acids (LCPUFA) from 18-carbon PUFA. (fatsoflife.com)
None of these small polymorphisms can be clearly assigned to changes in the amino acid sequence of the FADS enzymes, and are believed to mostly influence the regulation of gene expression. (fatsoflife.com)
This genetic variant, termed an indel (insertion/deletion mutation), was found to influence the regulation of the expression levels of both FADS-1 and FADS-2 in a cellular system, with the minor allele in Japanese people being associated with lower expression of the FADS-1 and FADS-2 genes. (fatsoflife.com)
Gene co-expression networks are widely studied in the biomedical field, with algorithms such as WGCNA and lmQCM having been developed to detect co-expressed modules. (biomedcentral.com)
Moreover, this method is designed not only for gene co-expression networks but can also be applied to any general fully connected weighted network. (biomedcentral.com)
Among these biomedical networks, gene co-expression network is one of the most widely studied. (biomedcentral.com)
Gene co-expression networks are constructed by gene expression profiles and in which each gene is represented by a node and the relationship between a pair of gene is represented by a connected edge. (biomedcentral.com)
The strength of the relationship between genes is usually quantified by the correlation between the expression of two genes. (biomedcentral.com)
Gene co-expression networks are divided into weighted and unweighted networks. (biomedcentral.com)
An unweighted gene co-expression network is a traditional binary network, which only keeps relationships between genes above a specified cutoff, while a weighted network is a fully connected network and keeps all relationships as a continuous measurement. (biomedcentral.com)
Because setting a cutoff will cause the information loss, weighted gene co-expression networks are commonly used in biomedical analysis [ 12 ]. (biomedcentral.com)
To get biologically relevant information, it is necessary to perform module (or community) detection in gene co-expression networks. (biomedcentral.com)
Unfortunately, the existing WGCNA and lmQCM can only detect gene co-expression modules without the ability to incorporate such prior knowledge. (biomedcentral.com)
Introduction: We hypothesized that common Alzheimer's disease (AD)-associated variants within the triggering receptor expressed on myeloid (TREM) gene cluster influence disease through gene expression. (nottingham.ac.uk)
Spots that appear under the tissue are assigned to clusters by Space Ranger and are determined using only gene expression information, and without any spatial information from the image. (10xgenomics.com)
See the Gene/Feature Expression mode section of the Navigation tutorial to learn more about how to construct your own lists. (10xgenomics.com)
The dark red spots correspond to high expression for this gene. (10xgenomics.com)
The first step to creating the CA1 cluster is to filter spots to retain only those with high expression of Fibcd1 . (10xgenomics.com)
Based on the Log2 Max Exp scale at the bottom of the Gene Expression panel, we will set a threshold of 3. (10xgenomics.com)
The LCR interacts with β-globin gene cluster involving long range DNA interactions mediated by various transcription factors to drive the regulation of globin genes expression. (kcl.ac.uk)
We found that the clusters decomposed by CPM outperformed MCL and MCODE as the candidates of disease-related clusters with well-supported biological significance in biological process, molecular function and cellular component of Gene Ontology (GO) and expression of human tissues. (ijbs.com)
With the increase in availability of human protein interaction data and gene expression data, the focus of bioinformatics development has shifted from understanding networks encoded by model species to understanding the networks underlying human disease [ 1 ]. (ijbs.com)
Integrating known disease genes with physical or biomolecular networks and gene expression data to identify disease-related subnetworks can help us explain many genetic and environmental factors influencing a disease in the context of a smaller number of discrete subnetworks as well as the causes or effects of the disease phenotype. (ijbs.com)
3 ] proposed a method to detect disease-related gene modules or dysfunctional pathways based on global characteristics of interactome coupled with gene expression data. (ijbs.com)
4 ] presented an approach to causal gene prediction that was based on integrating PPI network data with gene expression data under a condition of interest. (ijbs.com)
5 ] assembled an endotoxin inflammatory response network by integrating functional interactions curated from the literature with gene expression information. (ijbs.com)
Genes whose expression levels rise and fall similarly in a large set of samples, may be considered coexpressed. (mdpi.com)
These duplicated genes maintain a high degree of sequence similarity, but differ greatly in their substrate specificity and tissue expression patterns. (biomedcentral.com)
Both genes show no homology to any known genes, but their expression profiles are very similar to those of TCL1 and TCL1b. (unife.it)
Gene expression data clustering is one of the important tasks of functional genomics as it provides a powerful tool for studying functional relationships of genes in a biological process. (iitj.ac.in)
A strong expression of the VfNOD-CCP2 gene only could be detected the interzone II-III region. (uni-bielefeld.de)
Afterward, some of the clinical and expression characteristics were analyzed between clusters. (bvsalud.org)
The mRNA expression-based NMF was used to reveal the potential role of platelet adhesion-related genes in COAD . (bvsalud.org)
tures and gene expression patterns. (lu.se)
immature cell is then subjected to negative selection to delete grouped based on their previously defined pheno- self-reactive cells before it leaves the BM to enter peripheral typic features, and a gene expression pattern for lymphoid organs, where it becomes a mature B cell [9]. (lu.se)
the gene expression profile during B lymphoid differentiation. (lu.se)
To reduce the risk of analyzing cell line- pathway can be divided into distinct stages based on the specific features, we used several representative cell lines for recombination status of the Ig genes and on the expression each of four major stages in B cell development: pro-B, pre-B, pattern of surface markers and the presence of intracellular proteins [1- 6]. (lu.se)
The two closest points are merged and the new cluster is represented by an unweighted(median) or weighted(center of mass) average of the two points in gene expression space. (lu.se)

A gene cluster is a group of two or more genes found within an organism's DNA that encode similar polypeptides, or proteins, which collectively share a generalized function and are often located within a few thousand base pairs of each other. (wikipedia.org)
If only a single copy of a gene existed in the genome of a species, the proteins transcribed from this gene would be essential to their survival. (wikipedia.org)
however, over a long, evolutionary time period, the genetic information in the duplicated copy may undergo additional and drastic mutations in which the proteins of the duplicated gene served a different role than those of the original essential gene. (wikipedia.org)
Over the long, evolutionary time period, the two similar genes would diverge so the proteins of each gene were unique in their functions. (wikipedia.org)
The four genes encode four of the five major third instar larval cuticle proteins. (caltech.edu)
To tackle this issue, the development of network-based methods has become an effective tool in analyzing complex relationships among great number of entities such as genes and proteins. (biomedcentral.com)
These clusters are critical for the function of many different proteins, including those needed for DNA repair and the regulation of iron levels. (medlineplus.gov)
A shortage of this enzyme prevents the normal production of proteins that contain Fe-S clusters, which disrupts a variety of cellular activities. (medlineplus.gov)
This sequence predicts three open reading frames sequentially coding for proteins of 134, 230, and 142 amino acids, followed by the potential start of the tolA gene. (duke.edu)
In addition to TCL1 and TCL1b, the human locus contains two additional genes, TCL1-neighboring genes (TNG) 1 and 2, encoding proteins of 141 and 110 aa, respectively. (unife.it)

At least five genes were shown to be essential for the synthesis of AHBA, five genes were determined to encode the modular type I PKS that uses AHBA as the starter unit, and 20 or more genes appear to govern modification of the polyketide-derived framework, and rifamycin resistance and export. (nih.gov)
Disruption of the PKS genes at the end of rifA abolished rifamycin B production and resulted in the formation of P8/1-OG, a known shunt product of rifamycin biosynthesis, whereas disruption of the orf6 and orf9 genes, which may encode deoxysugar biosynthesis enzymes, had no apparent effect. (nih.gov)
The mauB, mauA, and mauC genes encode the periplasmic methylamine dehydrogenase (MADH) large and small subunit polypeptides and amicyanin, respectively. (caltech.edu)
Physically linked clusters of genes that encode the enzymatic information for the synthesis of specialized metabolites are a well-established feature of microbial secondary metabolism. (bath.ac.uk)
Numerous gene clusters that encode for the biosynthesis of different classes of metabolite have now been discovered in a variety of plant species. (bath.ac.uk)

Our analyses also show that reported chimeric sequences of the CYP2D6 and CYP2D7 genes in the chimpanzee genome appear to be exchanged in its genome database. (go.jp)
BGDM Docker integrates a software for genome annotation (Prokka), a software for pan-genome analysis and classification (PanX) and a software dedicated to identify clusters of biosynthetic genes, along with the metabolites that can be produced from such clusters (anti-SMASH). (peerj.com)
In contrast, the biosynthesis of plant specialized metabolites has until recently been thought to be almost exclusively encoded by genes that are randomly scattered in the genome. (bath.ac.uk)
Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. (nature.com)
Because of their location in the swine genome and their implication in reproductive physiology, this gene cluster was characterized and evaluated for effects on reproductive traits in swine. (biomedcentral.com)

Salmonella genomic island 1 (SGI1) contains an antibiotic resistance gene cluster and has been previously identified in multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, and Paratyphi B. We identified a variant SGI1 antibiotic-resistance gene cluster in a multidrug-resistant strain of S. enterica serovar Albany isolated from food fish from Thailand and imported to France. (cdc.gov)
Genetic organization of the antibiotic resistance gene cluster of Salmonella genomic island 1 (SGI1) of Salmonella enterica serovar Typhimurium DT104 and serovar Albany strain 7205.00. (cdc.gov)
The antibiotic resistance genes are clustered in part of a 43-kb genomic island called Salmonella genomic island 1 (SGI1), located between the chromosomal thdf and int2 genes ( 6 , 7 ). (cdc.gov)
The close genomic locations of these two genes as well as their functional similarity have hindered efforts to define whether each gene independently influences human triglyceride concentrations. (doe.gov)
Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. (nature.com)
Sequence analysis of a genomic VfNOD-CCP1 clone isolated revealed the presence of one intron seperating a first exon encoding the signal peptide from a second exon encoding the cysteine cluster domain of this nodulin. (uni-bielefeld.de)

A gene family is a set of homologous genes within one organism. (wikipedia.org)
Genes found in a gene cluster may be observed near one another on the same chromosome or on different, but homologous chromosomes. (wikipedia.org)
This family is comprised of three genes that are 55-60% homologous in DNA sequence and clustered within 8 kb of DNA. (caltech.edu)
Quantitative trait loci (QTL) for age of puberty, nipple number and ovulation rate have been identified in Meishan crosses on pig chromosome 10q (SSC10) near the telomere, which is homologous to human chromosome 10p15 and contains an aldo-keto reductase (AKR) gene cluster with at least six family members. (biomedcentral.com)
The homologous region on mouse chromosome 13 contains a cluster of eight or nine AKR1C genes [ 12 ]. (biomedcentral.com)
To aid in the development of a mouse model we also have characterized the murine Tcl1 locus and found five genes homologous to human TCL1b. (unife.it)

In the course of subsequent evolution, they diverge, so that the products they code for have different but related functions, with the genes still being adjacent on the chromosome. (wikipedia.org)
however, rather than the Hox cluster and the ParaHox cluster resulting from a cluster containing three genes, the Hox cluster and ParaHox cluster were as a result of single gene tandem duplication, identical genes found adjacent on the same chromosome. (wikipedia.org)
Cis-duplication, or intrachromosomal duplication, entails the duplication of genes within the same chromosome whereas trans duplication, or interchromosomal duplication, consists of duplicating genes on neighboring but separate chromosomes. (wikipedia.org)
This gene is found in the small histone gene cluster on chromosome 6p22-p21.3. (nih.gov)
Downstream of the retron sequence is the yidY gene, which is also found in the chromosome of other S. enterica serovars ( 7 ). (cdc.gov)
CYP2D6 belongs to the CYP2D subfamily, a gene cluster located on chromosome 22, which comprises the CYP2D6 gene and pseudogenes CYP2D7P and CYP2D8P . (go.jp)
Members of the apolipoprotein gene cluster (APOA1/C3/A4/A5) on human chromosome 11q23 play an important role in lipid metabolism. (doe.gov)
The analysis was carried out using five restriction fragment length polymorphism markers on chromosome 11 inside the β-globin cluster using the restriction enzymes HincII and HindIII. (wayne.edu)
In the human, an aldo-keto reductase (AKR) gene family (AKR1C) has been identified near the telomere on chromosome 10p15 that contains at least six aldo-keto reductase family 1, member C genes [ 11 ]. (biomedcentral.com)
TCL1 and TCL1b genes on human chromosome 14q23.1 are activated in T cell leukemias by translocations and inversions at 14q32.1, juxtaposing them to regulatory elements of T cell receptor genes. (unife.it)

Therefore, identifying the mechanisms responsible for the regulation of these genes in patients with COAD has become important. (bvsalud.org)

Sequence comparisons indicate it arose by an unequal crossing over event involving two closely related and adjacent cuticle genes. (caltech.edu)
cloning of the structural gene, sequence analysis and inferred domain structure of the multifunctional enzyme. (microbiologyresearch.org)
The nucleotide sequence of the methylamine utilization (mau) gene region from Methylobacterium extorquens AM1 was determined. (caltech.edu)
Scholars@Duke publication: Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous bacteriophages into Escherichia coli. (duke.edu)
Sequence analysis of mutant fii genes identified the 230-amino acid protein as the fii gene product. (duke.edu)
Comparison of sequence data with the porcine BAC fingerprint map show that the cluster of genes resides in a 300 kb region. (biomedcentral.com)
Comparative genomics analysis of human sequence variation in the UGT1A gene cluster. (uchicago.edu)
Apart from the multiple presence of the common nodulin motifs AAAGAT and CTCTT on both DNA strands of the putative VfNOD-CCP1 promoter region a sequence element resembling the organ specific element of the soybean lbc3 gene promoter was identified. (uni-bielefeld.de)

Rough-fuzzy clustering for grouping functionally similar genes from microarray data. (iitj.ac.in)

Cancer datasets normally contain a small size of samples while each sample has a large number of genes as features. (mun.ca)
This takes little RAM, allowing you to cluster a large number of genes, but the clustering results could be inferior to those obtained with e.g. average linkage. (lu.se)

Mutations in fii or tolA of the fii-tolA-tolB gene cluster at 17 min on the Escherichia coli map render cells tolerant to high concentrations of the E colicins and do not allow the DNA of infecting single-stranded filamentous bacteriophages to enter the bacterial cytoplasm. (duke.edu)

In recent years, many studies had shown the utility of these networks in extracting disease-related clusters/subnetworks [ 2 ] and inferring disease-causing genes [ 2 , 7 - 11 ]. (ijbs.com)

Most microbial BGCs that have been identified so far contain genes encoding core biosynthetic enzymes such as polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS). (hindawi.com)
Several independent gene clusters containing varying lengths of type I polyketide synthase genes were isolated from 'Streptomyces nanchangensis' NS3226, a producer of nanchangmycin and meilingmycin. (microbiologyresearch.org)
We have cloned and sequenced polyketide synthase (PKS) genes from the aclacinomycin producer Streptomyces galilaeus ATCC 31,615. (nih.gov)

a , Maximum-likelihood tree using concatenated protein sequences of 100 genes randomly selected from 4,694 Fusarium orthologous genes that have clear 1:1:1:1 correlation among the Fusarium genomes and have unique matches in Magnaporthe grisea , Neurospora crassa and Aspergillus nidulans . (nature.com)
Clustering of gene ontology terms in genomes. (lu.se)
Essential is a word that should always be used with caution because such thing does not exist in phage genomes (unlike ribosomal genes and tRNA synthetases in bacteria for example). (edu.au)
We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. (pacb.com)
Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species. (pacb.com)

Here, we conducted a preliminary study to investigate the evolution and gene organization of the CYP2D subfamily, focused on humans and four non-human primates (chimpanzees, orangutans, rhesus monkeys, and common marmosets). (go.jp)
Their organization as well as their protein sequences showed high similarity to those of other type II PKS genes. (nih.gov)

Scholars@Duke publication: Synaptic clustering of AMPA receptors by the extracellular immediate-early gene product Narp. (duke.edu)
Narp (neuronal activity-regulated pentraxin) is a secreted immediate-early gene (IEG) regulated by synaptic activity in brain. (duke.edu)

however, gene duplication allows essential genes to undergo mutations in the duplicated copy, which would ultimately give rise to new genes over the course of evolution. (wikipedia.org)
Jointly, these two sets of data support the hypothesis that advantageous mutations within the FADS gene cluster occurred prior to human migration out of Africa (~85 kya), and swept to fixation within African but not European or Asian populations. (blogspot.com)
Myopathy with deficiency of iron-sulfur cluster assembly enzyme is caused by mutations in the ISCU gene. (medlineplus.gov)
Mutations in the ISCU gene severely limit the amount of iron-sulfur cluster assembly enzyme that is made in cells. (medlineplus.gov)
which means both copies of the gene in each cell have mutations. (medlineplus.gov)
The phenotype resulting from an insertion of the chloramphenicol gene into the gene coding for the 142-amino acid protein is identical to that of mutations in fii and tolA. (duke.edu)
Further investigations are necessary to identify these mutations and understand how these AKR1C genes affect these important reproductive traits. (biomedcentral.com)
These researchers have successfully identified many rare Mendelian disorders that are caused by mutations in one gene. (the-scientist.com)

When gene duplication occurs to produce a gene cluster, one or multiple genes may be duplicated at once. (wikipedia.org)
Although common diseases tend to cluster within families, they are influenced by an interaction of environmental factors and multiple genes. (the-scientist.com)

The antibiotic resistance gene cluster represents approximately one third of SGI1 and is located at the 3´ end of the structure ( 6 , 7 ). (cdc.gov)
Moreover, variant SGI1 antibiotic resistance gene clusters have recently been reported for serovars Typhimurium DT104 and Agona variant SGI1 ( 12 , 15 ). (cdc.gov)

As a linear projection of the data into 2 dimensions does not scale well in the number of clusters there is a need for new visualization techniques using non-linear arrangement of the clusters. (uni-muenchen.de)
While Loupe Browser provides visualization of clusters determined by Space Ranger, it is possible to define your own clusters based on gene markers. (10xgenomics.com)

Putative regulatory genes were also identified. (nih.gov)
Rifamycin production in A. mediterranei is governed by a single gene cluster consisting of structural, resistance and export, and regulatory genes. (nih.gov)

pHZ1358 was shown to be generally useful for generating mutant strains by gene disruption and replacement in NS3226 as well as in several other Streptomyces strains. (microbiologyresearch.org)

These gene clusters include the Hox gene cluster, the human β-globin gene cluster, and four clustered human growth hormone (hGH)/chorionic somaomammotropin genes. (wikipedia.org)
Conserved gene clusters, such as Hox and the human β-globin gene cluster, may be formed as a result of the process of gene duplication and divergence. (wikipedia.org)
β-Globin Gene Cluster Haplotypes in the Corsican and Sardinian Populations " by Veronica Latini, Lucia Vacca et al. (wayne.edu)
We report an infant with sickle cell disease phenotype by biochemical analysis whose β-globin gene (HBB) sequencing showed sickle cell mutation (HBB S ) heterozygosity. (kcl.ac.uk)
Further analyses revealed that proband's duplicated β-globin gene cluster (∼650 kb) encompassing HBB A does not include the immediate upstream locus control region (LCR) or 3′ DNase I hypersensitivity (HS) element. (kcl.ac.uk)
Is there a role for CTCF binding sites in regulating the structure or function of the a globin gene cluster? (ox.ac.uk)

In this project, we conduct a comprehensive study by examining widely used clustering, feature selection, and classification methods, and applying them to different cancer datasets including Colon, Leukemia and, Lymphoma. (mun.ca)
By applying scHiCluster to simulated and real single-cell Hi-C data, for example, the authors demonstrate that the approach can bump up the Hi-C clustering accuracy of low-coverage datasets, making it possible to pick up topologically-associating domain-like structures in individual cells. (genomeweb.com)

Several SNPs located in the FADS gene cluster are now known to be related to changes in risk for complex and chronic diseases. (fatsoflife.com)
Since genes associated with similar diseases/disorders show an increased tendency for their protein products to interact with each other through protein-protein interactions (PPI), clustering analysis obviously as an efficient technique can be easily used to predict human disease-related gene clusters/subnetworks. (ijbs.com)
Common, complex diseases such as diabetes, asthma, and cardiovascular conditions are the next challenge gene hunters face. (the-scientist.com)
Analytical strategies that have successfully mapped the rare monogenic disorders have not definitively identified any genes involved in complex diseases. (the-scientist.com)

Model based clustering approaches have emerged as statistically well grounded methods, but the properties of these algorithms when applied to large-scale data sets are not always well understood. (ugent.be)

However, recent reports highlight the growing number of examples of gene clusters for specialized metabolic pathways in plants. (bath.ac.uk)
The gene copy number and enrichment analysis results revealed that two pathways were differentially enriched. (bvsalud.org)

We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. (hindawi.com)
Using a human liver cell culture model, SimuGen has demonstrated that with the correct choice of biomarkers, empiric functional data analysis models, and higher level exploratory analysis such as clustering (based on the models), it is possible to predict and describe liver toxicity with greater sensitivity than animal tests. (cam.ac.uk)
Each entry shows the average adjusted Rand index of the original clustering result with clusters from remeasured data. (biomedcentral.com)
A high average adjusted Rand index means that clusters from remeasured data are in close agreement with clusters from the original data. (biomedcentral.com)
By testing on TCGA data, our novel method can provide more complete coverage of genes, more balanced module size and finer granularity than current methods in detecting modules with significant overall survival difference. (biomedcentral.com)
Evaluating image data and clustering in the spatial view. (10xgenomics.com)
High platelet counts are associated with worse survival in real-world patients , and alternations to platelet adhesion-related genes have resulted in poorer prognoses , based on online data. (bvsalud.org)

A collection of distinct equivalent clusterings can be summarized as a weighted graph on the set of genes, from which we extract fuzzy, overlapping clusters using a graph spectral method. (ugent.be)

Species who have gene clusters have a selective evolutionary advantage because natural selection must keep the genes together. (wikipedia.org)
In the case of the Hox gene, a shared ancestral ProtoHox cluster was duplicated, resulting in genetic clusters in the Hox gene as well as the ParaHox gene, an evolutionary sister complex of the Hox gene. (wikipedia.org)
LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. (nature.com)

This segment lies at chromosomal location 44D and contains two small gene families. (caltech.edu)

The biosynthesis of SMs is controlled by enzymes encoded by biosynthetic gene clusters (BGCs). (hindawi.com)
The involvement of some of the genes in the biosynthesis of rifamycin B was examined. (nih.gov)
Studies on polymorphisms found in one cluster of closely-located genes coding for fatty acid desaturases (FADS), enzymes that play an important role in the biosynthesis of both omega-6 and omega-3 LCPUFA, are providing an interesting perspective on the interaction between traditional diets and the population genetic history of humans. (fatsoflife.com)
Accordingly, when aclacinomycins minimal PKS genes were substituted for those of nogalamycin in the plasmid carrying genes for auramycinone biosynthesis, aklavinone was produced in the heterologous hosts. (nih.gov)

The cores of these fuzzy clusters contain tight sets of strongly coexpressed genes, while the overlaps exhibit relations between genes showing only partial coexpression. (ugent.be)
Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. (mdpi.com)

Now, I don't doubt that there was selection in Africans at the FADS gene cluster. (blogspot.com)
Population-based differences in LC-PUFA levels and their product-to-substrate ratios can, in part, be explained by polymorphisms in the fatty acid desaturase (FADS) gene cluster, which have been associated with increased conversion of MC-PUFAs to LC-PUFAs. (blogspot.com)
Here, we show evidence that these high efficiency converter alleles in the FADS gene cluster were likely driven to near fixation in African populations by positive selection ~85 kya. (blogspot.com)
Positive Selection of an Indel Polymorphism in the FADS Gene Cluster May be Driving Long-Chain PUFA Biosynthetic Capacity in Specific Human Populations. (fatsoflife.com)
In 2012, a much larger, 22-base pair long stretch of nucleotides was identified within a part of the FADS-2 gene that is not translated to protein (an intron). (fatsoflife.com)

A GO annotation analysis shows that these local maxima are all biologically equally significant, and that simultaneously clustering genes and conditions performs better than only clustering genes and assuming independent conditions. (ugent.be)
Two systems were developed for functional analysis of the gene clusters by gene disruption or replacement. (microbiologyresearch.org)
Computer analysis showed that the MauG polypeptide contains two putative heme binding sites and that the MauM and MauN polypeptides have four and two FeS cluster signatures, respectively. (caltech.edu)
Sun PG, Gao L, Han S. Prediction of Human Disease-Related Gene Clusters by Clustering Analysis. (ijbs.com)
Then, the differentially expressed platelet adhesion-related genes of COAD were analyzed using the TCGA database, and patients were further classified by employing the non-negative matrix factorization (NMF) analysis method . (bvsalud.org)
Based on platelet adhesion-related genes , patients with COAD were classified into two clusters by NMF-based clustering analysis . (bvsalud.org)
Subsequent differentiation allows for rear- analysis of a set of mouse B lineage cell lines rep- rangements of the Ig light-chain (IgL) genes that replace the resenting defined stages of B cell development us- surrogate light-chain genes on the surface of the B cell [8]. (lu.se)

Currently bioassay sets must be exported (support exists already in BASE 2.1) for clustering. (lu.se)

The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. (pacb.com)
Screening the porcine CHORI-242 BAC library with a full-length AKR1C4 cDNA identified 7 positive clones and sample sequencing of 5 BAC clones revealed 5 distinct AKR1C genes ( AKR1CL2 and AKR1C1 through 4 ), which mapped to 126-128 cM on SSC10. (biomedcentral.com)

Loupe Browser provides the capability to calculate new statistically significant genes for the user defined categories using two options provided at the bottom of the Categories mode. (10xgenomics.com)

thus it is located between the thdf gene and the yidY gene of their chromosomes ( 6 , 14 ). (cdc.gov)

Also, clustering with absolute correlation as the distance metric does not work very well at all. (lu.se)

In addition to the minimal PKS, the cloned region included the PKS genes for polyketide ketoreductase (aknA), aromatase (aknE1) and oxygenase (aknX), as well as genes putatively encoding an aklanonic acid methyl transferase (aknG) and an aklanonic acid methyl ester cyclase (aknH) for post-polyketide steps were found. (nih.gov)

Here we find that in the developing mouse and human brain POGZ binds predominantly euchromatic loci and these are enriched for human neurodevelopmental disorder genes and transposable elements. (biorxiv.org)
A molecular characterization of this strain is reported, which includes the finding of a transposable element in the promoter region of the unexpressed gene. (caltech.edu)

Gene therapy approaches are attractive alternatives where the most vulnerable immune cells are modified with antiviral small RNAs with the goal to engineer an HIV-resistant immune system. (ca.gov)

however, the resulting protein of each gene is distinctive from the resulting protein of another gene within the cluster. (wikipedia.org)
Eleven kb away from the cuticle gene cluster lies another gene family. (caltech.edu)

Neighborhood graphs allow for visual assessment of relationships between adjacent clusters. (uni-muenchen.de)

We also found that most of the disease-related clusters consisted of tissue-specific genes that were highly expressed only in one or several tissues, and a few of those were composed of housekeeping genes (maintenance genes) that were ubiquitously expressed in most of all the tissues. (ijbs.com)

Comparison of amino acid sequences of polypeptides encoded by mau genes from M. extorquens AM1, P. denitrificans, and Thiobacillus versutus shows that they have considerable similarity. (caltech.edu)

Although its basic precursors (3-amino-5-hydroxy benzoic acid AHBA, and acetic and propionic acids) had been established, and several biosynthetic intermediates had been identified, very little was known about the origin of AHBA nor had the PKS and the various genes and enzymes that modify the initial intermediate been characterized. (nih.gov)

Nuetzmann, H-W & Osbourn, A 2014, ' Gene clustering in plant specialized metabolism ', Current Opinion in Biotechnology , vol. 26, pp. 91-9. (bath.ac.uk)

A set of 34 genes clustered around the rifK gene encoding AHBA synthase were defined by sequencing all but 5 kilobases (kb) of a 95 kb contiguous region of DNA from A. mediterranei. (nih.gov)
We found that one gene cluster - consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase - is present in all strains that grow in medium with methionine as sole sulfur source. (pacb.com)

The protein products of this gene cluster play an important role in the transport of large molecules such as the E colicins and filamentous phage DNA into the bacterium. (duke.edu)

Fruhling M, Albus U, Hohnjec N, Geise G, Pühler A, Perlick AM. A small gene family of broad bean codes for late nodulins containing conserved cysteine clusters. (uni-bielefeld.de)

Anatomy19

Organisms21

Diseases2

Chemicals and Drugs52

Analytical, Diagnostic and Therapeutic Techniques and Equipment30

Phenomena and Processes139

Disciplines and Occupations3

Technology, Industry, Agriculture3

Information Science7

Health Care2

Algorithm11

Abstract2

Expression52

Proteins10

Encode5

Genome5

Genomic6

Homologous6

Chromosome10

Regulation1

Sequence8

Microarray data1

Large number of genes2

Bacterial1

Disease-causi1

Polyketide synthase3

Genomes5

Organization2

Synaptic2

Mutations8

Multiple genes2

Antibiotic2

Visualization2

Regulatory genes2

Streptomyces1

Globin Gene6

Datasets2

Diseases4

Algorithms1

Pathways2

Data7

Spectral1

Evolutionary3

Chromosomal1

Biosynthesis4

Coexpression3

FADS5

Analysis7

BioAssay1

Distinct2

Statistically1

Chromosomes1

Correlation1

Ketoreductase1

Transposable2

Approaches1

Another gene2

Adjacent1

Tissue-specific1

Similarity1

Enzymes1

Metabolism1

Synthase2

Phage1

Small gene1