• 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)
  • The biosynthesis of SMs is controlled by enzymes encoded by biosynthetic gene clusters (BGCs). (hindawi.com)
  • Metabolic gene clusters or biosynthetic gene clusters are tightly linked sets of mostly non-homologous genes participating in a common, discrete metabolic pathway. (wikipedia.org)
  • Genome mining for biosynthetic gene clusters (BGCs) has become an integral part of natural product discovery. (wikipedia.org)
  • 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)
  • One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification of cross-species patterns that can be matched to the presence of metabolites or biological activities. (wikipedia.org)
  • The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. (nih.gov)
  • Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (nih.gov)
  • Prior to the "genomic era," when the acquisition of DNA sequence involved significant labor and expense, the sequencing of genes was strongly linked to the experimental characterization of their products. (plos.org)
  • however, current genomic selection genotyping tools have a paucity of genetic markers within key immune gene clusters (IGC) involved in the cattle innate and adaptive immune systems. (usda.gov)
  • A genome-wide analysis of the D. melanogaster genome found that differences in TE density across 50 kb genomic regions was due both to transposition and duplication. (biomedcentral.com)
  • At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. (biomedcentral.com)
  • The analysis of 50 kb genomic windows identified 23 regions with a high density of TE insertions, most of them located in pericentromeric regions or on chromosome 4 [ 1 ]. (biomedcentral.com)
  • RIViT-seq technology could speed up associating transcription factors with their target genes. (doe.gov)
  • The newly identified IL-2 target genes include many genes previously linked to apoptosis in other cellular systems that may contribute to IL-2-dependent survival functions. (torvergata.it)
  • The degree of methylation affects the expression of target genes and has a significant impact on cell proliferation, apoptosis, cytokine secretion, and cell activity ( 6 , 7 ). (frontiersin.org)
  • There were 3954 correlations and a total of 15 correlations for differentially expressed proteins (DEPs) and differentially expressed genes (DEGs) from proteomics and transcriptomics. (hindawi.com)
  • To identify key genes differentially expressed in the human retinal pigment epithelium (hRPE) following low-level West Nile virus (WNV) infection. (molvis.org)
  • 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)
  • Bortoluzzi S, Alessi FD, Romualdi C, Danieli GA: Differential expression of genes coding for ribosomal proteins in different human tissues. (karger.com)
  • The main applications in statistical data analysis include clustering proteins and ordering genes. (umu.se)
  • Defects in genes and proteins important for B cell maturation block the maturation on certain stage and cause primary immunodeficiencies ( IDbase ). (lu.se)
  • Bioinformatic analysis of the proteomes revealed shared Gene Ontology (GO) terms and signaling pathways within the clusters of co-expressed proteins (Tables 1-3 and S4. (lu.se)
  • 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)
  • Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. (biomedcentral.com)
  • Based on the results of bioinformatics analysis, we propose a possible mechanism for the transcriptional regulation of the human DHRS4 gene cluster. (biomedcentral.com)
  • A strongly hydrophilic region was predicted at positions from 30 to 50 of the An-peNPV Polh protein by bioinformatics analysis. (scirp.org)
  • Additionally, we provide evidence that many genes expressed in T cells locate in chromosomal clusters, and that select IL-2-regulated genes are located in at least two clusters, one at 5q31, a known cytokine gene cluster, and the other at 6p21.3, a region that contains genes encoding the tumor necrosis factor (TNF) superfamily members TNF, LT-alpha and LT-beta. (torvergata.it)
  • In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters. (biomedcentral.com)
  • These changes usually disrupt the regulation of many oncogenes or tumor suppressor genes in tumors, resulting in their abnormal expression. (biomedcentral.com)
  • The main emphasis is on supervised machine learning methods for classification and prediction of tumor gene expression profiles. (lu.se)
  • ABSTRACT: The polyhedrin (polh) gene is often used to analyse evolution of baculovirus. (scirp.org)
  • In this study, we present integrated quantitative proteome, transcriptome, and methylome analyses of hematopoietic stem cells (HSCs) and four multipotent progenitor (MPP) populations. (lu.se)
  • To define the divergence in gene expression modules between C(3) and C(4) photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C(4)) and Tarenaya hassleriana (C(3)), by RNA sequencing. (nih.gov)
  • Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. (imperial.ac.uk)
  • The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. (imperial.ac.uk)
  • The overarching aim of the Epigenetics common cause of gastric cancer, Pan-cancer genoMe and Group (EGE) is to advance the which is the third most common cause tranScriPtoMe analySiS and understanding of the role of epigenetic of cancer-related deaths worldwide. (who.int)
  • Gene ontology (GO) term enrichment analysis was used to highlight the most relevant GO terms associated with a given gene list following toxin exposure. (plos.org)
  • The overall IFN-related gene panel annotated by gene ontology (GO) showed an excellent diagnostic capacity in CD4+ T cells (Sensitivity = 0.82, specificity = 0.82 and AUC = 0.90), while IFI44L , another IFN-related gene not annotated by GO, showed high prediction ability in both CD4+ (AUC = 0.86) and CD8+ (AUC = 0.75) T cells. (frontiersin.org)
  • 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)
  • Metabolic gene clusters are common features of bacterial and most fungal genomes. (wikipedia.org)
  • Methods We selected bacterial artificial chromosome (BAC) clones harboring key IGC genes from public and private libraries and sequenced the inserts with long-read sequencing technologies. (usda.gov)
  • Scientists have previously identified clusters of bacterial genes that are particularly good at producing therapeutics. (eurekalert.org)
  • Members of the apolipoprotein gene cluster (APOA1/C3/A4/A5) on human chromosome 11q23 play an important role in lipid metabolism. (doe.gov)
  • The pfhrp2 gene is located on chromosome 8 of the parasite genome, and a paralogous gene ( pfhrp3 ) is located on chromosome 13. (cdc.gov)
  • 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)
  • The FGG gene is found on chromosome 4 . (medlineplus.gov)
  • Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. (biomedcentral.com)
  • Prior to December of 2008, an examination of the DHRS4 gene on chromosome 14q11.2 in GenBank revealed that the human DHRS4 gene cluster consisted of two genes, DHRS4 and DHRS4L2 . (biomedcentral.com)
  • This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. (nih.gov)
  • This gene is found in the large histone gene cluster on chromosome 6. (nih.gov)
  • KEGG enrichment and gene set enrichment analysis (GSEA) showed that a large number of genes were enriched in inflammatory immune-related pathways, such as the toll-like receptor signaling pathway. (frontiersin.org)
  • 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)
  • Horizontal gene cluster transfer has been linked to ecological niches in which the encoded pathways are thought to provide a benefit. (wikipedia.org)
  • 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)
  • Clusters of co-expressed and co-localized genes have been recognized as playing key roles in a number of functional pathways and adaptive responses including organism development, differentiation, disease states and aging. (nottingham.edu.cn)
  • orthogonal exPeriMental changes and pathways induced by EGE investigated the impact of aSSeSSMent of ePigenetic environmental factors in cancer causation, both current H. pylori infection and driver geneS and their link to underpinning studies of etiology e , pigenetic memory of past (eradicated) environMental carcinogenS carcinogen evaluation, and prevention. (who.int)
  • Transcriptomics focuses on gene transcription and regulation of transcription in cells [ 25 , 26 ]. (hindawi.com)
  • Based on the analysis of gene transcripts and bioinformatic prediction, we propose here that antisense transcription may be involved in the transcriptional initiation regulation of DHRS4 and in the posttranscriptional splicing of DHRS4L2 and DRHS4L1 for the homologous identity of DHRS4 gene cluster. (biomedcentral.com)
  • To investigate the transcription of DHRS4L1 and the transcriptional regulation of DHRS4 gene cluster, we cloned the full length RNA variants of DHRS4L1 in this study, and found that DHRS4L1 initiated its transcription from two TSS, exon a2 and exon 1. (biomedcentral.com)
  • Data analysis from preprocessing to clustering and basics of inferring gene regulation. (helsinki.fi)
  • The aim of this study is to perform an in silico analysis of T3SS-2, and to compare it with other known T3SSs. (pasteur.fr)
  • In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. (biomedcentral.com)
  • Functional annotation clustering of the microarray data showed that gene clusters involved in immune and antiviral responses ranked highly, involving genes such as chemokine (C-C motif) ligand 2 ( CCL2 ), chemokine (C-C motif) ligand 5 ( CCL5 ), chemokine (C-X-C motif) ligand 10 ( CXCL10 ), and toll like receptor 3 ( TLR3 ). (molvis.org)
  • TNF-alpha induced increased expression of genes coding mediators of apoptosis, cell-matrix interactions, proteolysis and C-C chemokines. (cdc.gov)
  • This data will be used in genome-wide association analyses to identify suitable genetic markers to track disease resistance phenotypes in dairy cattle. (usda.gov)
  • Mutations in the FGG gene can lead to congenital afibrinogenemia, a condition that causes excessive bleeding due to the absence of fibrinogen protein in the blood. (medlineplus.gov)
  • Most FGG gene mutations that cause this condition lead to an abnormally short blueprint for protein formation (mRNA). (medlineplus.gov)
  • Mutations in one or both copies of the FGG gene can cause other bleeding disorders known as hypofibrinogenemia, dysfibrinogenemia, or hypodysfibrinogenemia. (medlineplus.gov)
  • As a scientist she has been involved in mapping the human genome and identifying genes and mutations, which give rise to heritable disorders. (bepress.com)
  • Patients with Allgrove syndrome (type 2 FGD) have no mutations in the coding sequence or the promoter region of this receptor gene. (medscape.com)
  • Antimicrobial resistance occurs through different mechanisms, which include spontaneous (natural) genetic mutations and horizontal transfer of resistant genes through deoxyribonucleic acid (DNA). (who.int)
  • We conducted an integrative analysis of the multiple-autoimmune disease methylation dataset including GD, RA, SLE, and SSc samples, to identify the common methylation patterns of autoimmune diseases. (frontiersin.org)
  • In conclusion, our study demonstrated that hypomethylation of IFN-related genes is a common feature of GD/RA/SLE/SSc patients in CD4+ T cells, and the DNA methylation profile of IFN-related genes could be promising biomarkers for the diagnosis of GD, RA, SLE, and SSc. (frontiersin.org)
  • DNA methylation is one of the major epigenetic mechanisms, and it plays an important role in determining gene function ( Hedrich and Tsokos, 2011 ). (frontiersin.org)
  • DMRs show continuous gain or loss of methylation during differentiation, and the overall change in DNA methylation correlates inversely with gene expression at key loci. (lu.se)
  • Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα−) breast tumors. (biomedcentral.com)
  • Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. (biomedcentral.com)
  • The study revealed that persistent estrogen-mediated LRES leads to recruitment of H3K27me3 repressive chromatin marks, which are accompanied by accumulation of DNA methylation in a gene cluster located at 16p11.2. (biomedcentral.com)
  • Epigenetics refers to the study of heritable changes in gene function without alterations in DNA sequence ( Bird, 2007 ). (frontiersin.org)
  • Comparative genomics analysis of human sequence variation in the UGT1A gene cluster. (uchicago.edu)
  • In the minus strand of the human DHRS4 gene cluster, a gene transcribed in an antisense direction was found containing a 5' sequence overlapping the region of exon 1 and promoter of DHRS4 . (biomedcentral.com)
  • cloning of the structural gene, sequence analysis and inferred domain structure of the multifunctional enzyme. (microbiologyresearch.org)
  • It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. (csc.fi)
  • This knowledge meant the scientists could focus on searching for certain types of gene clusters in samples rather than having to sequence and analyse the whole genomes of bacteria. (eurekalert.org)
  • RESULTS: Ninety LAB isolated from fermented cabbage were identified as species of Lactobacillus and Leuconostoc, whereas 115 clones of the 16S rRNA gene sequence from fermented cabbage DNA were identified as Lactobacillus, Weissella, Pediococcus and Leuconostoc. (who.int)
  • 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)
  • 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)
  • 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)
  • Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
  • As the sequencing and gene annotation projects of entire genomes of many species are headed towards completion (see, e.g. [13] ), massive mapping efforts in biology are now focused on how the genes interact. (lu.se)
  • In addition to specialized metabolite genes, we show that the ArcZ regulon affects approximately 15% of all transcripts in Photorhabdus and Xenorhabdus . (nature.com)
  • Analysis of exon composition in the transcripts of DHRS4 gene cluster revealed that exon 1 was absent in all the transcripts initiated from exon a1 of DHRS4L2 and exon a2 of DHRS4L1 . (biomedcentral.com)
  • Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. (nih.gov)
  • Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. (nih.gov)
  • Since genes are composed of a given alphabet (A, T, C, G) with fixed pairing properties A-T and C-G, probes can be constructed that attract gene transcripts extracted from cell tissues and cultures. (lu.se)
  • The molecular interactions of genes and gene products underlie fundamental questions of biology. (lu.se)
  • 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)
  • Interpretation is supported by customized resources, including module-level analysis workflows, fingerprint grid plot visualizations, interactive web applications and an extensive annotation framework comprising functional profiling reports and reference transcriptional profiles. (imperial.ac.uk)
  • 3 Institute of Developmental Genetics, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany. (nih.gov)
  • I also learned how to find different genes in the clusters and how to visualize them. (csc.fi)
  • To form fibrinogen, the γ chain attaches to the fibrinogen A alpha (Aα) and fibrinogen B beta (Bβ) chains, each produced from different genes. (medlineplus.gov)
  • Quantitative real-time PCR analysis of 23 genes was used to validate the microarray results. (molvis.org)
  • 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)
  • The homologous comparison analysis suggests that DHRS4 , DHRS4L2 and DHRS4L1 are three homologous genes in human. (biomedcentral.com)
  • 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)
  • 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)
  • Toxicogenomics is a relevant approach for the identification of biomarkers associated with toxicity and can be employed in endpoint analysis following exposure to DNTs. (plos.org)
  • How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? (lu.se)
  • Background: The notion that genes are non-randomly organized within the chromosomes of eukaryotic organisms has recently received strong experimental support. (nottingham.edu.cn)
  • MIBiG, BiG-FAM Bioinformatic tools have been developed to predict, and determine the abundance and expression of, this kind of gene cluster in microbiome samples, from metagenomic data. (wikipedia.org)
  • Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. (bvsalud.org)
  • More recently, nine roo insertions were also described in the promoter region of another stress response gene, CG18446 that encodes a nucleic acid binding protein [ 10 ]. (biomedcentral.com)
  • This gene is intronless and encodes a replication-dependent histone that is a member of the histone H1 family. (nih.gov)
  • In addition, IGS sequencing (e.g., sequencing of intergenic regions between the 16S and 23S rRNA genes) has been used to taxonomy studies, while partial sequencing of the gene gtfB , which encodes the enzyme glucosyltransferase B, has been used to investigate enzymatic activity and virulence 11-12 . (bvsalud.org)
  • 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)
  • 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)
  • In addition, in order to phenotypically anchor the gene expression data, changes in the heterogeneity of cell subtype populations and cell cycle phase were monitored using flow cytometry. (plos.org)
  • The authors declare that the sponsors had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
  • 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)
  • 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)
  • 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)
  • 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)
  • Our data reveal the differential expression landscape of 493 transcription factors and 682 lncRNAs and highlight specific expression clusters operating in HSCs. (lu.se)
  • Course: Single-cell RNA-seq data analysis with Chipster, Section: 8. (csc.fi)
  • This means rapid iterations while exploring for emergent behavior, and full programmability of the filtering and clustering steps.Conclusions: Gepoclu is a useful data-mining tool for exploring relationships among transcriptional data deriving form different sources. (nottingham.edu.cn)
  • On the applied side, she has elaborated methods based on topological data analysis for high-throughput screening of nanoporous crystalline materials, classification and synthesis of neuron morphologies, and classification of neuronal network dynamics. (epfl.ch)
  • This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. (csc.fi)
  • If you don't have these skills, you might like to attend the course Single cell RNA-seq data analysis with Chipster instead. (csc.fi)
  • Previous data has reported similarity between human brain and testis gene expression patterns. (karger.com)
  • Typically when data are presented, the fluor- escent intensity from the tissue is pseudo-colored red and the intensity from the reference green, and the logarithmic ratio of background corrected red and green intensities for each gene (spot) is subject to analysis (see Fig. 1 ). (lu.se)
  • Pseudotime analysis - Using the selection tool, the user traces a path through the data which uses this information to define the start and stop clusters for a slingshot analysis. (lu.se)
  • All the authors have approved the review procedure, data analysis, reporting and submission of the analysis outcomes. (who.int)
  • Gepoclu provides expression-based gene selection from multiple experimental sources, position-based gene clustering and cluster visualization functionalities, all as parts of the same fully integrated, and interactive, package. (nottingham.edu.cn)
  • Putative regulatory genes were also identified. (nih.gov)
  • Some Pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second T3SS (T3SS-2) in addition to the well characterized Hrc1 T3SS which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. (pasteur.fr)
  • Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C(4) bundle sheath cells. (nih.gov)
  • Analyses cell clusters of a single-cell RNA-sequencing experiment to get pathway-level expressions for every cluster of cells. (rdrr.io)
  • In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. (biomedcentral.com)
  • Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. (biomedcentral.com)
  • By cloning the full length of RNA variants through 5'RACE and 3'RACE, we identified two transcription start sites, within exon a2 and exon 1, of this newly named gene DHRS4L1 using neuroblastoma cell line BE(2)-M17. (biomedcentral.com)
  • Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division. (karger.com)
  • Low-level WNV infection of hRPE cells induced expression of genes that are typically associated with the host cell response to virus infection. (molvis.org)
  • To view the results, click on 2D-DIGE analysis of B cell maturation. (lu.se)
  • A total of 2063 protein spots across eight human B cell lines were clustered on the basis of the relative protein abundance ( Supplementary Figure 1 and S2). (lu.se)
  • Related to analyse_sc_clusters in reactome/ReactomeGSA . (rdrr.io)
  • These Unigenes represent a wide range of genes classified according to their characterization and function. (karger.com)
  • Results: Characterization using RAPD markers uncovered significant genetic variability among the samples and indicated the existence of clusters, which allowed us to reconstruct both the origin and clinical history of the disease. (bvsalud.org)
  • Sun PG, Gao L, Han S. Prediction of Human Disease-Related Gene Clusters by Clustering Analysis. (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)
  • 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)
  • 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)
  • Transcription factor networks arcs - The menu for toggling the lines between common pairs of genes in transcription factor networks has been improved. (lu.se)
  • Rifamycin production in A. mediterranei is governed by a single gene cluster consisting of structural, resistance and export, and regulatory genes. (nih.gov)
  • Metabolic gene clusters are also involved in nutrient acquisition, toxin degradation, antimicrobial resistance, and vitamin biosynthesis. (wikipedia.org)
  • A region in cluster A (∼133 kb) seemed to be involved in nanchangmycin production because replacement of several DNA fragments in this region by an apramycin resistance gene [ aac3(IV) ] gave rise to nanchangmycin non-producing mutants. (microbiologyresearch.org)
  • This report presents the status of AMR in Africa by analysing the main types of resistance and the underlying genes where possible. (who.int)
  • METHODS: Culture-dependent and -independent (16S rRNA gene clone libraries were constructed) methods were used to determine the composition of LAB in fermented cabbage. (who.int)
  • We found that the most significant differentially methylated sites had a remarkable enrichment in type I interferon (IFN) pathway genes. (frontiersin.org)
  • 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)
  • S. Gomi, C. E. Zhou, W. Y. Yih, K. Majima, Maeda S. (1997) Deletion analysis of four of eighteen late gene expression factor gene homologues of the baculovirus, BmNPV. (scirp.org)
  • Based on phylogenetic analysis and gene organization comparisons, the T3SS-2 cluster of the P. syringae pv. (pasteur.fr)
  • Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (nih.gov)
  • Based on phylogenetic analysis, we suggest that the presence of multiple roo insertions in this region is likely to be the result of several bursts of transposition. (biomedcentral.com)
  • It has since been demonstrated that metabolic gene clusters can arise in a genome by genome rearrangement, gene duplication, or horizontal gene transfer, and some metabolic clusters have evolved convergently in multiple species. (wikipedia.org)
  • Therefore, the integrative analysis across different autoimmune diseases may reveal more clues about the pathogenesis. (frontiersin.org)
  • 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)
  • The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. (nih.gov)
  • We found that known C(4) genes were recruited to photosynthesis from different expression domains in C(3), including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. (nih.gov)
  • Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. (nih.gov)
  • Hence, it means that human testis could also play a crucial role in human speciation if these two tissues exhibit similar gene expression patterns. (karger.com)
  • Determining the large scale anatomy of gene expression patterns of various human tissues could draw a more convincing conclusion, and better our understanding of the correlation/inter-correlation among different tissues. (karger.com)
  • Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. (karger.com)
  • Present results provide evidence to support the proposal that human testis and brain share the highest similarity of gene expression patterns. (karger.com)
  • Based on the genetic similarity of the isolates and pattern of amino acid variations identified by partial sequencing of the gtfB gene, base-pair changes were identified and correlated with different virulence patterns among the isolates. (bvsalud.org)
  • Conclusions: The partial sequencing of the gtfB gene can be a useful tool for elucidating the colonization patterns of S. mutans . (bvsalud.org)
  • Streamlining Regulon Identification in Bacteria Regulons are a group of genes that can be turned on or off by the same regulatory protein. (doe.gov)
  • Histidine-rich protein 2/3 antigen concentrations were reduced with corresponding gene deletions. (cdc.gov)
  • The FGG gene provides instructions for making the fibrinogen gamma (γ) chain, one piece (subunit) of the fibrinogen protein. (medlineplus.gov)
  • 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)
  • Currently bioassay sets must be exported (support exists already in BASE 2.1) for clustering. (lu.se)
  • These additional T3SS gene clusters define a subgroup within the Rhizobium T3SS family. (pasteur.fr)
  • The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (nih.gov)