• While almost all cells in an organism contain the entire genome of the organism, only a small subset of those genes is expressed as messenger RNA (mRNA) at any given time, and their relative expression can be evaluated. (wikipedia.org)
  • The original designs of most of the PCR primers used for the analysis of 16S rRNA genes were based on known sequences deposited in public databases. (frontiersin.org)
  • For example, a complete 16S rRNA gene sequence can be obtained by analyzing the sequences of genomes or large genome fragments, providing taxonomic information along with information on other functional genes. (frontiersin.org)
  • The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)
  • The sequence analysis of the 32-35,000 predicted genes indicates the there may be as many as 1,000 kinase or kinase-like genes. (ddw-online.com)
  • Analysis of gene expression can include measuring expression levels of a small set of genes to whole genome expression monitoring. (ddw-online.com)
  • 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)
  • Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
  • The ability of genes or alleles to affect the representation of the host organism in a biome is an operational definition for the "function" of the gene (in that context). (genomicglossaries.com)
  • Bioinformatics is limited to sequence, structural, and functional analysis of genes and genomes and their corresponding products and is often considered computational molecular biology. (limswiki.org)
  • This analysis resulted in the identification of motifs upstream of several genes involved in central metabolism, sulfate assimilation, and energy metabolism, as well as genes potentially encoding acetate permease. (umass.edu)
  • The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. (osti.gov)
  • However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. (osti.gov)
  • Genome-wide analysis of gene expression provides insight into the transcriptional state of a cell or tissue sample, measuring RNA levels for thousands of genes in parallel. (biomedcentral.com)
  • In addition, gene-expression data need to be compared between species, signifying the need to link genes from different organisms. (biomedcentral.com)
  • Here we harnessed the potential of RNA sequencing in 89 human pancreatic islet donors to identify genes and exons regulated in this relevant tissue for T2D. (nih.gov)
  • Using Affymetrix Gene Chip analysis, we have identified genes linked to regenerative success downstream of BMP signalling, including the BMP inhibitor Gremlin and the stress protein Hsp60 ( no blastema in zebrafish). (biomedcentral.com)
  • Gene Ontology analysis showed that genes involved in embryonic development and growth are significantly over-represented in regenerating early hindlimb buds and that successful regeneration in the Xenopus hindlimb correlates with the induction of stress response pathways. (biomedcentral.com)
  • Gene Ontology analyses showed that undifferentiated keratinocytes were characterised by genes for motility and the adaptive immune response. (ox.ac.uk)
  • Release 2.0 provides exclusive access to microarray expression data from Saccharomyces cerevisiae and Rattus norvegicus, as well as curated information on approximately 700 genes from various organisms. (ox.ac.uk)
  • Microarray analysis is one such powerful method that is widely used to identify genes that are expressed differently in two or more conditions (disease vs. normal). (bvsalud.org)
  • To better understand the function of the altered genes, gene ontology and pathway analysis are performed. (bvsalud.org)
  • The analysis at gene level is often complemented by interrogating the data in a broader biological context that considers as unit of measure groups of genes that may have a common function or biological trait. (bvsalud.org)
  • As breast cancer is a multistage progression disease resulting from a genetic sequence of mutations, understanding the genes whose expression values increase or decrease monotonically across pathologic stages can provide insightful clues about how breast cancer initiates and advances. (bvsalud.org)
  • Current cancer research makes use primarily of DNA microarrays in which an arrayed series of microscopic spots of pre-defined DNA oligonucleotides known as probes are covalently attached to a solid surface such as glass, forming what is known as a gene chip. (wikipedia.org)
  • DNA microarrays evolved from Southern blotting which allows for detection of a specific DNA sequence in a sample of DNA. (wikipedia.org)
  • Use of resequencing microarrays to Influenza viruses are a major cause of respiratory infec- detect single nucleotide polymorphisms and generate pri- tions in humans and result in substantial illness, death, mary sequences enables identification of genetic variants and economic problems throughout the world. (cdc.gov)
  • DNA microarrays take advantage of the major feature of the DNA double helix, the sequence complementarity of the two-paired strands, by using DNA capture probes which are the complement of the expressed target sequence (mRNA, cRNA or cDNA made from the mRNA). (ddw-online.com)
  • Two of the most common uses of the DNA microarrays are genetic analysis and the analysis of gene expression. (ddw-online.com)
  • This report will focus in using DNA microarrays for the analysis of gene expression or expression profiling, and how DNA chips are used for drug discovery and development. (ddw-online.com)
  • In what follows we limit ourselves to the analysis of gene expression measurements obtained using microarrays with small spots of DNA fixed to glass slides. (lu.se)
  • By physically restraining bound molecules against an antibody array, they capture both transient interactions, which yeast two-hybrid or tandem mass spectrometry methods don't, and weak interactions, which are usually obliterated by the wash in protein-DNA microarrays. (genomeweb.com)
  • This study aimed at the identification of prognostic gene expression markers in early primary colorectal carcinomas without metastasis at the time point of surgery by analyzing genome-wide gene expression profiles using oligonucleotide microarrays. (biomedcentral.com)
  • Gene expression profiling was performed using Whole Human Genome 4x44K Oligonucleotide Microarrays. (biomedcentral.com)
  • BACKGROUND: Gene-wise differential expression is usually the first major step in the statistical analysis of high-throughput data obtained from techniques such as microarrays or RNA-sequencing. (bvsalud.org)
  • Glass is by far the most common substrate for biomolecular arrays, including high-throughput sequencing flow cells and microarrays. (bvsalud.org)
  • The overarching goal of this new approach is to translate the knowledge learned from a systematic, global analysis of genomic data into a complete understanding of biology. (usuhs.edu)
  • After sequencing the human genome, numerous projects have focused on characterizing genomic alterations and associating them with the different diseases or functional elements of the genome. (biomedcentral.com)
  • Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing. (cdc.gov)
  • DNA labeled with fluorophores (target) is prepared from a sample such as a tumor biopsy and is hybridized to the complementary DNA (cDNA) sequences on the gene chip. (wikipedia.org)
  • The level of fluorescence at a particular spot provides quantitative information about the expression of the particular gene corresponding to the spotted cDNA sequence. (wikipedia.org)
  • To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A) tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA) synthesis and sequencing to eliminate potential biases caused by mismatching of polymerase chain reaction (PCR) primer sequences. (frontiersin.org)
  • These results clearly demonstrate that poly(A) tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities. (frontiersin.org)
  • Array probes are produced by polymerase chain reaction (PCR) amplification of selected cDNAs or designed on the basis of cDNA or gene sequence information. (biomedcentral.com)
  • Expressed sequence tag (EST) sequencing projects have generated millions of cDNA sequences for human, mouse and other organisms that are identified by an accession number in databases such as GenBank. (biomedcentral.com)
  • These include cDNA clone libraries, Affymetrix GeneChips, and oligonucleotide sets for human, mouse and rat (Table 1 ). (biomedcentral.com)
  • Reverse transcription was performed with SSII (Life Technologies), whose terminal transferase activity allows incorporation of a PCR binding site at the 3' end of the cDNA using a template-switching oligonucleotide (custom synthesized from Exiqon) as a template. (nih.gov)
  • Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
  • Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)
  • Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)
  • sequence variants ( 5-7 ) from viral, bacterial, and eukary- otic genomes ( 8-13 ). (cdc.gov)
  • The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)
  • Numerous studies on natural microbial communities from a variety of environments have been undertaken using 16S rRNA gene sequencing mediated by polymerase chain reaction (PCR) with oligonucleotide primers. (frontiersin.org)
  • In most cases, however, circulating strains, novel strains emerge sporadically this technology has relied on specific amplification of a because of reassortment in the segmented influenza RNA limited number of target sequences before hybridization, genome and have resulted in devastating influenza pan- thus restricting throughput and limiting final identification demics ( 1-3 ). (cdc.gov)
  • Considering the current limitations of NGS technology, full-length 16S rRNA gene sequences are better suited to downstream analytical methods such as fluorescence in situ hybridization. (frontiersin.org)
  • Array-based technologies measure hybridization signal intensities in one or two channels for each array feature or probe, resulting in absolute or relative information about the expression levels of the corresponding transcripts in the samples. (biomedcentral.com)
  • The frequencies of CNVs in these populations were analyzed by oligonucleotide array comparative genome hybridization, quantitative PCR, PCR, DNA sequencing across breakpoints, and single-worm PCR. (biomedcentral.com)
  • Using photolithographic in situ synthesis of DNA, we show that dipodal silanes are compatible with phosphoramidite chemistry and that hybridization performed on the resulting arrays provides greatly improved signal and signal-to-noise ratios compared with surfaces functionalized with monopodal silanes. (bvsalud.org)
  • As simultaneously identified and typed all component strains an alterative, high-density oligonucleotide resequencing of the trivalent FluMist intranasal vaccine. (cdc.gov)
  • The early expression profiles of these Trichoderma strains were studied after 20 h of incubation in the presence of tomato plants, using a high-density oligonucleotide (HDO) microarray, and compared to the profiles in the absence of plants. (microbiologyresearch.org)
  • Early studies of DNA melting and reformation were carried out in aqueous solutions and yielded important information about the dependence of melting temperature (Tm) on the G+C composition and salt concentration, as well as information on the dependence of the rate of reassociation on the sequence complexity of the nucleic acid. (ddw-online.com)
  • Rapid and comprehensive analysis of putative proteinous allergens ( allergenome ) by applying such a proteomic strategy … With allergenomics, we can not only detect and assign the putative allergens (proteins specifically interacting with IgE antibodies in a patient's blood) in a short time, but also analyze the quantitative and qualitative change of the antigens, depending on the surroundings and environmental conditions of an allergenic causative. (genomicglossaries.com)
  • Fig. 1: Photochemistry of light-oxygen-voltage receptors and sequences of proteins under study. (nature.com)
  • Grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses ( e.g. , homology-based prediction of structure or function). (biomedcentral.com)
  • In an attempt to adapt resequencing microarray technol- ceptibility, and viral escape from vaccine-elicited immu- ogy to surveillance and diagnostics, we developed the res- nity, continually surveying the genetic composition (i.e., piratory pathogen microarray (RPM) version 1 for primary sequence) of circulating and emerging variants is detection and sequence typing of 20 common respiratory necessary. (cdc.gov)
  • Genetic analysis includes procedures for genotyping, SNP (single nucleotide polymorphism) detection, strain identification and various other procedures. (ddw-online.com)
  • Unlike such genetic changes, epigenetic changes, which do not alter genome sequence, can result in three possible outcomes: passive dilution, active repair through negative feedback, or active maintenance through positive feedback. (nature.com)
  • EN] DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. (upv.es)
  • There are several kinds of genetic testing methods that uncover varying depths of information to examine the genome, the full collection of genetic information of an organism. (hello100.com)
  • Bioconductor packages edgeR (version 3.10.0 ) and ChIPpeakAnno (version 3.2.0) for transcriptome quantification, differential gene expression analysis and annotation. (nih.gov)
  • GermOnline, a fully operational prototype subject-oriented knowledgebase designed for community annotation and array data visualization, is accessible at http://www.germonline.org. (ox.ac.uk)
  • The traditional approach to the study of biology employs small-scale experimentation that results in the description of a molecular sequence of known function or relevance. (usuhs.edu)
  • EN] A nanoporous anodic alumina (NAA)-based sensor system for the detection of Mycoplasma was developed through the implementation of "molecular gates" selective to the presence of this bacterium. (upv.es)
  • Bioinformatics now entails the creation and advancement of databases, algorithms, computational, and statistical techniques and theory to solve formal and practical problems arising from the management and analysis of biological data. (limswiki.org)
  • Microbial DNA was extracted from subgingival dental plaque (n=281) and V3-V4 regions of the 16S rRNA gene were sequenced to measure the relative abundances of 20 a priori - selected taxa with nitrate‐reducing capacity. (ahajournals.org)
  • SAGE results in quantitative information connected to 10-14 base-pair (bp) sequence tags derived from the 3' ends of transcripts. (biomedcentral.com)
  • Qualitative and quantitative analysis of circulating DNA is a promising noninvasive tool. (upv.es)
  • We applied two strategies to eliminate or substantially reduce the obstacles of tRNA modification and structure for efficient and quantitative tRNA sequencing ( Fig. 1a ). (cdc.gov)
  • To compare experiments that are performed on these different platforms, array probes and sequence tags need to be linked. (biomedcentral.com)
  • Cross-referencing array probes allows comparison of studies carried out using different technologies, and facilitates validation of gene expression. (biomedcentral.com)
  • In addition, the database can be used to annotate array probes with reference sequences and updated gene descriptions from UniGene. (biomedcentral.com)
  • Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. (osti.gov)
  • C. Peterson, M. Ringne´r / Artificial Intelligence in Medicine 28 (2003) 59-74 structure and function, cellular metabolism, development of cells and tissues, and response of organisms to their environments. (lu.se)
  • Each oligo has a 30-base-pair randomly generated sequence, flanked by a barcode that allows multiplexing and Illumina adapters. (genomeweb.com)
  • Sequencing was done on the Illumina GAII platform. (nih.gov)
  • ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library LL-I1 were mapped to the human genome using Pash. (nih.gov)
  • ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library LL-I1 were processed into density graphs of raw signal representing the aligned read density. (nih.gov)
  • The data was generated by deep sequencing using Illumina HiSeq 2000. (nih.gov)
  • RNA libraries were prepared for sequencing using standard Illumina protocols. (nih.gov)
  • Sequencing was performed using the Illumina MiSeq v2 500cycle or NovaSeq 6000 SP platform. (cdc.gov)
  • Techniques include DNA microarray technology or sequenced-based techniques such as serial analysis of gene expression (SAGE). (wikipedia.org)
  • Due to lowering costs, RNA-Sequencing is becoming more common as a method for cancer gene expression profiling. (wikipedia.org)
  • Gene expression analysis may uncover or facilitate answers to these questions as well as assist research and development and health care in several other ways. (ddw-online.com)
  • To further characterize pathways involved in naphthalene degradation in NaphS2, the draft genome was sequenced, and gene and protein expression examined. (elsevierpure.com)
  • RESULTS: Draft genome sequencing, gene expression analysis, and proteomic analysis revealed that NaphS2 degrades naphthoyl-CoA in a manner analogous to benzoyl-CoA degradation. (elsevierpure.com)
  • microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. (cancerindex.org)
  • DNA microarray technology aids in gene expression analysis and other bioinformatics functions. (limswiki.org)
  • Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies, and the modeling of evolution. (limswiki.org)
  • Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis. (umass.edu)
  • Global gene-expression analysis is carried out using different technologies that are either array- or sequence-tag-based. (biomedcentral.com)
  • Recovery is also observed in most cases when double-stranded RNA is used to silence the same coding sequence in different regulatory contexts that drive germline expression. (nature.com)
  • We also observed from in vivo analysis that Velo knock-down flies exhibit significant upregulation of the AMP expression and reduced bacterial load. (cnrs.fr)
  • Gene over-expression analyses in Xenopus limb and tail regeneration have indicated that successful regeneration requires the re-activation of developmental FGF or BMP signalling pathways [ 8 - 12 ]. (biomedcentral.com)
  • Beyond this time, no differences in global gene expression in infected and control animals were detectable by microarray analysis. (biomedcentral.com)
  • High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)
  • Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. (cdc.gov)
  • Selective microfluidics-based ligand enrichment followed by sequencing, or SMiLE-seq, combines antibody arrays, mechanical trapping, and next-generation sequencing readouts to provide a new platform for characterizing DNA-protein interactions. (genomeweb.com)
  • CONCLUSIONS: We encourage the usage of the absmean (non-directional), mean (directional) and maxmean (directional) scores for roast GSA analysis as these are simple measures of enrichment that have presented dominant results in all provided analyses in comparison to the more complex KS measures. (bvsalud.org)
  • In addition to iden- sequencing produces accurate data, the requirement for tification, this method provided primary sequence informa- knowledge of template sequences and the inability to tion, which suggested that distinct lineages of influenza quickly process multiple targets hinder its practical appli- viruses co-circulated during the 2004-2005 season, and cation in epidemiologic and diagnostic investigations. (cdc.gov)
  • 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)
  • Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. (limswiki.org)
  • A Platform record is composed of a summary description of the array or sequencer and, for array-based Platforms, a data table defining the array template. (dry-lab.org)
  • CGHbase-1.58.0 CGHbase: Base functions and classes for arrayCGH data analysis. (fredhutch.org)
  • The pipeline overviews the steps in microarray analysis, such as data pre-processing, normalization, and statistical analysis using visualization techniques such as heatmaps, box plots, and so on. (bvsalud.org)
  • The GEO accession number for the sequencing data reported in this paper is GSE66550. (cdc.gov)
  • Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. (cdc.gov)
  • Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures. (limswiki.org)
  • Arguably one of the first "bioinformatics" projects-though the concept didn't yet exist-involved the 1965 creation and maintenance of a protein sequence database called the Atlas of Protein Sequence and Structure by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. (limswiki.org)
  • Single-end sequencing of 36 nucleotides was performed using a Genome Analyzer IIx. (nih.gov)
  • It looks at variations in the sequence of nucleotides, the basic units of the DNA, represented by letters " A " for Adenine, " T " for Thymine, " C " for Cytosine, and " G " for Guanine. (hello100.com)
  • Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm ( http://liulab.dfci.harvard.edu/MACS/ ). (nih.gov)
  • Computer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequence variants. (biomedcentral.com)
  • A DNA oligonucleotide array for duplex pathogen detection on a DVD platform is developed. (upv.es)
  • [3] [4] Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing . (limswiki.org)
  • Subsequently, 3' ligation adapter sequences were identified and removed from the reads. (nih.gov)
  • The genome sequence also suggests that NaphS2 may degrade other monoaromatic compounds. (elsevierpure.com)
  • Rare mutations in genome sequence that result from failed DNA repair are transmitted across generations through DNA replication during each cell division. (nature.com)
  • Cultures testing positive for Each tiled prototype sequence was selected to have an influenza A or B viruses were confirmed by using reverse intermediate level of sequence homology across a group of transcription-polymerase chain reaction (RT-PCR) analy- microbial or viral strains, which allowed for efficient sis with previously reported protocols ( 16,17 ). (cdc.gov)
  • SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now. (cdc.gov)
  • In general, a sequence-specific identifier (GenBank accession number) serves as a reference to the array probe sequence. (biomedcentral.com)
  • In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. (osti.gov)
  • There is ample evidence for the preservation of multiple gene copies due to selection for increased gene dosage in diverse organisms [ 20 ]. (biomedcentral.com)
  • The poly(A) tailing method indicated that Desulfobacterales were the predominant Deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. (frontiersin.org)
  • Final libraries were amplified by 12 cycles of PCR and sequenced on a NextSeq 500. (nih.gov)
  • Because of its large library of statistical R packages and user-friendly interface, the R programming language provides a platform for microarray analysis. (bvsalud.org)
  • Image analysis is the first crucial step to obtain reliable results from microarray experiments. (biomedcentral.com)
  • Here we report that a minimal combination of cis- regulatory sequences can support permanent RNA silencing of a single-copy transgene and its derivatives in C. elegans simply upon mating. (nature.com)
  • Coined in 1916, It refers to an ecological community of organisms and environments. (genomicglossaries.com)
  • Currently, GeneHopper contains the most commonly used array resources for human, mouse and rat. (biomedcentral.com)
  • Despite the fact that the latest NGS technologies enable reading only of relatively short sequence fragments (~500 bp), these so-called "deep sequencing" methods are still powerful tools that ultimately may enable researchers to obtain a more holistic understanding of microbial communities in their natural environments ( Fuhrman, 2009 ). (frontiersin.org)
  • Degradation of toluene and 2-methylnaphthalene, and the presence of at least one bss-like and bbs-like gene cluster in this organism, suggests that NaphS2 degrades both compounds via parallel mechanisms. (elsevierpure.com)
  • Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. (umass.edu)
  • Since mutations and reassortments are often to strains that retain primer-targeted sequences. (cdc.gov)
  • The sequences obtained using the poly(A) tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-PCR (RT-PCR) with published domain-specific primers. (frontiersin.org)
  • For SMiLE-seq, what the button captures is interactions between GFP-labeled transcription factors and a library of oligonucleotides. (genomeweb.com)