Genome sequence and gene expression. Medical search. Frequent questions

Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. (nature.com)
As increasing number of next-generation sequencing (NGS) datasets are being produced from various-omics initiatives, transcriptome sequencing of flora and fauna for a specific developmental stage/condition gains its popularity in biological research. (nature.com)
To understand how the genome and epigenome regulates cellular function, development of high-throughput sequencing methods, known as next-generation sequencing, are beginning to unravel genome-wide correlations between the genome, epigenome and transcriptome within a large population of cells or tissues. (confex.com)
To overcome this limitation, recent advances in molecular biology have enabled genome-wide single-cell measurements of the transcriptome, genome or certain epigenetic marks that capture this cell-to-cell heterogeneity. (confex.com)
In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)
They also used Illumina's HiSeq 2000 instrument to do transcriptome sequencing on tissue samples from house fly adults and larvae. (genomeweb.com)
Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. (lu.se)
New sequencing technology provides thorough characterization of the genome and transcriptome. (lu.se)

This research project attempts to identify the genetic determinants of SHRSP/Gla phenotypes by using mRNA and micro(mi)RNA expression profiling data, in combination with the genome sequence of the SHRSP/Gla and WKY/Gla, to facilitate human translational studies for hypertension and vice versa. (gla.ac.uk)
RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. (biomedcentral.com)
Given the exponential growth of the number of publicly available RNA-seq samples, we expect this approach will become especially relevant for studying the effects of tissue-specific and rare pathogenic genetic variants to aid clinical interpretation of exome and genome sequencing. (biomedcentral.com)
An extensive literature documenting physiological and ecological diversity make Daphnia an ideal model to study the genetic architecture of phenotypic variation in natural populations and the evolution of genome structure/function relationships in aquatic environments. (biomedcentral.com)
Notably, a large number of stress-related elements present in the promoter regions of some ZmCAMTA genes, indicating a genetic basis of stress expression regulation of these genes. (frontiersin.org)
Type I toxin-antitoxin (TA) systems are widespread genetic modules in bacterial genomes. (mdpi.com)
The researchers found that the daddy longlegs, also known as harvestmen, evolved their special legs not through a genetic secret ingredient but by reusing parts of the same genetic recipe found in other arthropods, such as genes that affect tarsomeres - subsegments of the leg. (npr.org)
To use and improve new biotechnologies involving human genome analysis and genetic mapping in the interests of risk-forecasting and the early diagnosis, prevention, prognosis and treatment of human diseases, particularly hereditary diseases and cancers, and with a view to a better understanding of the mechanisms of heredity. (europa.eu)
Because tissues are composed of several cell-types and even cells within the same cell-type have been shown to display dramatic cell-to-cell variability in gene expression, bulk measurements obscure quantification of how genetic or epigenetic features directly influence the function of individual cells. (confex.com)
and mutations in the genome's "dark matter" - genetic code that regulates the expression of other genes. (childrenshospital.org)
NEW YORK (GenomeWeb) - A Cornell University-led team has sequenced and started analyzing the genome of the domestic house fly, Musca domestica , in the hopes of detecting genetic clues for dealing with the pest and pathogens it carries. (genomeweb.com)
By spelling out protein-coding genes in the genome and comparing the house fly sequence to that of the fruit fly, Drosophila melanogaster , the team has endeavored to unravel genetic factors coinciding with house fly features. (genomeweb.com)
The house fly genome provides a rich resource for enabling work on innovative methods of insect control, for understanding the mechanisms of insecticide resistance, and genetic adaptation to high pathogen loads, and for exploring the basic biology of this important pest," corresponding author Jeffrey Scott, an entomology researcher at Cornell University, and his colleagues wrote. (genomeweb.com)
Moreover, given its ability to carry various pathogens without obvious detriments and to develop resistance to many of the insecticides that humans hurl at them, the house fly's genetic sequence is expected to offer hints about how it achieves these apparent forms of immunity. (genomeweb.com)
Next-generation sequencing has revolutionized the way researchers interrogate the genetic causes of rare single gene disorders. (aacc.org)
Dr. Shen, in your Perspective article you discuss the transformative effect of next-gen sequencing-based genetic testing, particularly exome and whole genome-based test on the molecular diagnostic practice. (aacc.org)
Recent high-impact research has shown the genomic/genetic differences between cancer and normal cells using methods such as next-generation sequencing [ 1 , 2 ]. (intechopen.com)
Both immunological and bacterial traits can be associated with genetic variants distributed across the mouse genome, making the CC a unique population for identifying specific host-pathogen genetic interactions that influence pathogenesis. (elifesciences.org)
The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection. (lu.se)
Entrez is NCBI's (the National Center for Biotechnology Information) database system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (lu.se)
Identifying genes on each chromosome is an active area of genetic research. (medlineplus.gov)
[ 2 , 3 ] Conventional techniques of gene investigation in cancer rely on the identification of single genetic alterations associated with disease. (medscape.com)

In this study, we performed a new bioinformatics analysis on microarray-based gene expression data obtained from the public domain to explore genes that were differentially induced by drugs between the group of capreomycin and PA-824 and the group of mainly the first-line TB drugs. (hindawi.com)
Detecting Staphylococcus aureus Virulence and Resistance Genes - a Comparison of Whole Genome Sequencing and DNA Microarray Technology. (cdc.gov)
The design and construction of a DNA microarray for any given microbial genome are straightforward. (medscape.com)
The introduction of complementary DNA (cDNA) microarray technology in 1995 has helped to facilitate the identification and classification of DNA sequence information and the assignment of functions to these new genes by allowing investigators to analyze expression of thousands of genes simultaneously in a single experiment. (medscape.com)
Because a microarray can be used to examine the expression of hundreds or thousands of genes at once, it promises to revolutionize the way gene expression is examined. (medscape.com)
This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. (medscape.com)

We were able to generate enough data to put together a human genome assembly that was in many respects superior to that initial draft," continued Paten, who currently oversees the Center for Big Data in Translational Genomics and is an assistant professor in the Department of Biomolecular Engineering at the University of California, Santa Cruz. (medscape.com)
In December 2017, Oxford Nanopore announced that Martin Smith, PhD, a researcher at the Kinghorn Centre for Clinical Genomics at the Garvan Institute, Darlinghurst, Australia, and colleagues were the first to sequence more than 1 million bases of continuous sequence using the MinION sequencer. (medscape.com)
Broad Genomics Platform sequences a whole human genome every four minutes. (broadinstitute.org)
In November 2022, Broad's Genomics Platform sequenced its 500,000th whole human genome, a mere four years after sequencing its 100,000th. (broadinstitute.org)
This project will use genomics to sequence and profile the germplasm in this national experiment, and participate in high intensity phenotypic evaluation with robotic measurement and analysis to understand how daily weather condition interact with genetics. (usda.gov)
Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. (hindawi.com)
In: Comparative genomics: Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families (D.Sankoff and J.H. Nadeau, eds. (umontreal.ca)
Each section was scanned using multispectral imaging and sequenced: whole-genome and targeted gene expression using the 10X Genomics human neuroscience panel. (speakerdeck.com)

Gene expression profiling is increasingly used in the field of infectious diseases for characterization of host, pathogen and the nature of their interaction. (cambridge.org)
The purpose of this study was to develop a robust, standardized method for comparative expression profiling and molecular characterization of Leishmania donovani clinical isolates. (cambridge.org)
Intracellular amastigote protocols need further refinement, but we describe a first generation tool for high-throughput comparative molecular characterization of patients' isolates, based on the changing expression profiles of promastigotes during in vitro differentiation. (cambridge.org)
Genome-assisted Identification, Purification, and Characterization of Bacteriocins. (uni-ulm.de)
Advances in sequencing technology have made characterization of genomes and gene expression products increasingly practical. (helsinki.fi)
Analysis of two highly expressed genes from Chlorella virus PBCV-1: Protein characterization and the DNA sequences of the major capsid protein gene and the early/late 33-kDa protein gene. (uml.edu)

CAMTAs participate in gene expression regulation by binding to the cis -elements in the promoter regions of numerous target genes. (frontiersin.org)
From an engineering perspective, gene expression regulation can be viewed as the output of a network of complex chemical and physical processes, and understanding how these processes interact and integrate to govern cellular phenotypes has been a major focus of my graduate and postdoctoral research. (confex.com)
Therefore, investigating the expression and regulation of miRNAs may elucidate the mechanism of gastric cancer. (hindawi.com)
The sequence data offered a peek at other fly features as well - from sex determination and sex-biased gene expression to house fly gene regulation. (genomeweb.com)

To further characterize pathways involved in naphthalene degradation in NaphS2, the draft genome was sequenced, and gene and protein expression examined. (elsevierpure.com)
Genes including the previously characterized NmsA, thought to encode an enzyme necessary for 2-methylnaphthalene metabolism, were not upregulated during growth of NaphS2 on naphthalene, nor were the corresponding protein products. (elsevierpure.com)
The protein sequences corresponding to the translations of coding sequences (CDS) in GenBank are collected for each GenBank release. (nih.gov)
This site contains the full taxonomy database along with files associating nucleotide and protein sequence records with their taxonomy IDs. (nih.gov)
This site contains all nucleotide and protein sequence records in the Reference Sequence (RefSeq) collection. (nih.gov)
About 30% of the human protein-coding genes are negatively regulated by miRNAs which suggests that they have a major role in regulating gene expression. (usda.gov)
Prediction of protein antigenic determinants from amino acid sequences. (scirp.org)
Transcription factors attach to noncoding DNA, regulating the expression of protein-coding genes. (stanford.edu)
1. Develop transferable DNA level models that predict gene expression and protein activity based on model systems and major crops. (usda.gov)
1. RNA expression and protein profiles will be developed for maize and other grasses under a wide range of abiotic conditions and tissues. (usda.gov)
These will be integrated and compared to other existing plant datasets to train machine learning models that accurately predict RNA expression and protein levels. (usda.gov)
The protein-protein interaction map specific to the rheumatoid arthritis pathophysiology and gene expression data in blood patient samples was used to discover a molecular signature of non-response to TNFi therapy. (springer.com)
Many of these genes encode proteins (e.g., enzymes involved in protein glycosylation) rarely associated with viruses. (uml.edu)
Using these DNA and RNA sequences, the team put together - and annotated - a 691 million base assembly that spans more than three-quarters of the fly's complete genome sequence and contains an estimated 14,810 protein-coding genes. (genomeweb.com)
[ 19 ] The apparent lack of a second-hit mutation in the genome of FLCs supports the role of DNAJB1-PRACA fusion protein as a major driver of this tumor and as a key diagnostic and therapeutic target. (medscape.com)
The bZIP protein sequence contains 2 conserved bZIP domains with a total length of ~ 60-80 amino acids. (biomedcentral.com)
Analyzing 5′-upstream non-protein-encoding regions of the human mitochondrial function-associated genes, we speculate that mitochondrial functions could be recovered or improved at a transcriptional level. (intechopen.com)
A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)
The student will be responsible for improving the annotations, especially for the untranslated regions that lie up and downstream of protein coding genes. (lu.se)
The protein produced from the ETV6 - PDGFRB fusion gene, called ETV6/PDGFRβ, functions differently than the proteins normally produced from the individual genes. (medlineplus.gov)
The ETV6 protein normally turns off (represses) gene activity and the PDGFRβ protein plays a role in turning on (activating) signaling pathways. (medlineplus.gov)
The ETV6/PDGFRβ protein is always turned on, activating signaling pathways and gene activity. (medlineplus.gov)

His interests include Bordetella molecular pathogenesis and gene expression bioinformatics. (medscape.com)

Given increasing numbers of RNA-seq samples in the public domain, we here studied to what extent eQTLs and ASE effects can be identified when using public RNA-seq data while deriving the genotypes from the RNA-sequencing reads themselves. (biomedcentral.com)
Even though these data originated from many different laboratories, samples reflecting the same cell type clustered together, suggesting that technical biases due to different sequencing protocols are limited. (biomedcentral.com)
That would not be enough to assemble a genome from scratch, but it is enough to start an analysis, especially as data continue to accumulate while the machine runs. (medscape.com)
This site provides full data records for CDD, along with individual Position Specific Scoring Matrices (PSSMs), mFASTA sequences and annotation data for each conserved domain. (nih.gov)
The DATA directory contains files listing all data linked to GeneIDs along with subdirectories containing ASN.1 data for the Gene records. (nih.gov)
Sample programs for manipulating gene data are provided in the tools directory. (nih.gov)
This site contains genome sequence and mapping data for organisms in Entrez Genome. (nih.gov)
Contains directories for each genome that include available mapping data for current and previous builds of that genome. (nih.gov)
Researchers from China and the US have produced the first broad benchmark of genomic and metagenomic assemblers specifically for PacBio HiFi sequence data. (genomeweb.com)
A blood-based molecular signature response classifier (MSRC) integrating next-generation RNA sequencing data with clinical features predicts the likelihood that a patient with rheumatoid arthritis will have an inadequate response to TNFi therapy. (springer.com)
The RNA is sequenced and the extensive amounts of data gained are analysed by novel algorithms. (helsinki.fi)
In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences. (sens.org)
Next-gen sequencing has also brought many changes in the way we do assay validation in the lab, the way we do data analysis, data interpretation, and the way we report the finding to the referring physicians. (aacc.org)
Recent advances in sequencing technology have produced sequence data covering the repetitive regions in the gaps and the first complete sequence of a human chromosome (X) was published in 2019 [ First complete sequence of a human chromosome ]. (blogspot.com)
Recent analyses of the whole genome sequencing data enable us to predict cancer incidence for healthy people at present. (intechopen.com)
Genome sequence data is deposited in the NCBI Gene Expression Omnibus (GEO), accession number GSE164156. (elifesciences.org)
Integrated analysis of transcriptomics data and DNA methylation data revealed concordant changes in gene expression. (cdc.gov)
Taking into account the clinical picture - transient attacks of hyperkinesis, their connection with movement, as well as data from video-electroencephalographic monitoring, a diagnosis of paroxysmal kinesiogenic dyskinesia was established, which in a further diagnostic search was confirmed by targeted sequencing of the pathological variant of the PRRT2 gene previously described in patients with kinesiogenic dyskinesia. (bvsalud.org)
Consolidating and exploring antibiotic resistance gene data resources. (cdc.gov)
We have extensive whole genome and RNA sequencing data taken from whole samples of flies at three life stages: larva, pupa and adult. (lu.se)
The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. (lu.se)
DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. (medscape.com)
Genomic sequencing will provide the data needed to unravel the complexities of the host-pathogen interaction. (medscape.com)
This hands on course will give you the experience and provide the tools that are needed to analyze next generation sequencing data. (lu.se)
After sequencing, data will be kept by CTG for 3 months and subsequently deleted . (lu.se)
Demultiplexed data files generated from the Illumina sequencing run. (lu.se)

One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune . (nature.com)
The Wnt genes encode secreted glycoprotein ligands that regulate a wide range of developmental processes, including axis elongation and segmentation. (biomedcentral.com)

Unexpectedly complex mitoribosomes in Andalucia godoyi , a protist with the most bacteria-like mitochondrial genome. (umontreal.ca)
Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids. (umontreal.ca)
Mitochondrial genomes of algae. (umontreal.ca)
Unusual mitochondrial genomes and genes. (umontreal.ca)
Mitochondrial Genome Evolution. (umontreal.ca)
Mitochondrial genome organization and evolution within the green algae and land plants. (umontreal.ca)
Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. (lu.se)

This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
During my graduate studies, I used a systems biology approach to demonstrate that chromatin environments at different genomic loci decouple transcription factor mediated initiation of gene expression from subsequent gene activation 6 . (confex.com)
As they reported online today in Genome Biology , the researchers pooled genomic DNA from half a dozen female house flies, using it as a template to generate sequence reads that were then assembled into a 691 million base M. domestica genome. (genomeweb.com)
In: Expressed sequence tags - generation and analysis, Methods in Molecular Biology Vol. 533 (J. Parkinson, ed. (umontreal.ca)

Many other molecular paramaters such as global or alelle-specific DNA methylation, gene expression levels, and microRNA expression levels can also be considered. (columbia.edu)
More recently, next-gen sequencing has been rapidly moving into the clinical diagnostic arena and transforming the practice of molecular diagnostic testing. (aacc.org)
So, many changes brought by next-gen sequencing are transforming the molecular diagnostic practice. (aacc.org)
METHODS: We have studied a consanguineous family with whole exome sequencing (WES) and performed in depth analysis of cryptic splicing on the molecular level using RNA. (bvsalud.org)
Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation. (cdc.gov)
Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. (medscape.com)
By understanding the molecular details of this interaction, we can identify virulence-associated microbial genes and host-defense strategies and characterize the cues to which they respond and mechanisms by which they are regulated. (medscape.com)
The pace of gene discovery rapidly accelerates, but its potential for explaining life at the molecular level remains largely unrealized because our understanding of gene function lags increasingly far behind. (medscape.com)

Sequence and Annotation of the 288-kb ATCV-1 Virus That Infects an Endosymbiotic Chlorella Strain of the Heliozoon Acanthocystis Turfacea. (uml.edu)
Sequence and Annotation of the 314-Kb MT325 and the 321-kb FR483 Viruses That Infect Chlorella Pbi. (uml.edu)
Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A. (uml.edu)
Several independent high-throughput methods for differential gene expression (including SAGE and differential display) may enable function annotation of sequenced genomes [ 2 ] . (medscape.com)

they can combine with the promoter regions of key genes in signaling pathways to regulate their transcription levels and, in turn, plant resistance to stress. (biomedcentral.com)
Global analysis of Mtb transposon mutant fitness (TnSeq) across the CC panel revealed that many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen's genome that has been maintained to ensure fitness in a diverse population. (elifesciences.org)

Using limma we identified differentially expressed genes between the pathology groups in the gray matter of the cortex only. (speakerdeck.com)

List of sequenced bacterial genomes List of sequenced animal genomes List of sequenced eukaryotic genomes List of sequenced fungi genomes List of sequenced plant genomes List of sequenced algae genomes Brayton KA, Lau AO, Herndon DR, Hannick L, Kappmeyer LS, Berens SJ, et al. (wikipedia.org)
The small sequencing devices have been used previously to track the Ebola and Zika epidemics, but the human genome is many orders of magnitude larger than those bacterial and viral genomes, making this "a huge technical achievement," Benedict Paten, PhD, one of the collaborators in the latest sequencing effort, told Medscape Medical News . (medscape.com)

Further, while cell-to-cell heterogeneity in gene expression has been shown to drive dramatic phenotypic variations, the upstream epigenetic mechanisms regulating this heterogeneity remain largely unknown 8 . (confex.com)
To elucidate whether epigenetic effects play a role for these gene expression changes, we performed whole genome bisulphite sequencing to assess DNA methylation patterns in the lungs 56 days after exposure to MWCNTs. (cdc.gov)
Taken together, the present study revealed that MWCNTs exert epigenetic effects in the lungs of exposed animals, potentially driving the subsequent gene expression changes. (cdc.gov)

Identification of genes involved in toluene degradation in NaphS2 led us to determine that NaphS2 degrades toluene, a previously unreported capacity. (elsevierpure.com)
Identification of sequence variations in the miRNA -target interactions may be particularly useful for rainbow trout breeding programs. (usda.gov)
Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L. (biomedcentral.com)
Identification of Subtypes in Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer Reveals a Gene Signature Prognostic of Outcome. (lu.se)

Researchers completed the first draft of the human genome sequence almost 20 years ago. (medscape.com)
This year, an international research team reported that they completed the human genome sequence using handheld nanopore devices in about 2 months at a cost of around $30,000. (medscape.com)
Eric Topol, MD, founder and director of the Scripps Translational Science Institute in La Jolla, California, seconds that statement, noting that many people thought it would take years before the human genome sequence could be assembled inexpensively from small machines. (medscape.com)
STRs make up about 5% of the human genome. (stanford.edu)
Approximately 3% of the human genome codes for miRNA sequences, which can suppress gene expression by mediating translational repression [ 5 ]. (hindawi.com)
Sandwalk: The 20th anniversary of the human genome sequence: 2. (blogspot.com)
It's been 20 years since the first drafts of the human genome sequence were published. (blogspot.com)
These first drafts from the International Human Genome Project (IHGP) and Celera were far from complete. (blogspot.com)
International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. (blogspot.com)
We've known for many decades that the correct size of the human genome is close to 3,200,000 kb or 3.2 Gb. (blogspot.com)
It's now possible to complete the human genome reference sequence by sequencing at least one individual but I'm not sure that the effort and the expense are worth it. (blogspot.com)
Morton, N.E. (1991) Parameters of the human genome. (blogspot.com)
Ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facies (MIM: 618527) stem from ELOVL1 gene deficiency in human. (bvsalud.org)
Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. (cdc.gov)
As of August 10, 2000, draft sequence was available for 87% of the human genome (https://www.ncbi.nlm.nih.gov/genome/seq/), and at least 39 prokaryotic genomes, including those of more than a dozen human pathogens, had been completely sequenced https://www.tigr.org/tdb/mdb/mdbcomplete.html). (medscape.com)
Read Mapping: alignment of reads to a specified reference genome (human, mouse or rat). (lu.se)

Relative to the fruit fly, the house fly genome contained far more repetitive sequence elements and copy number variants, the researchers noted, along with an especially robust representation of immune system components. (genomeweb.com)
it has the possibility of detecting causal variants in genes that are not previously known to be associated with the disease. (aacc.org)
INTRODUCTION: Next generation sequencing technologies allow detection of very rare pathogenic gene variants and uncover cerebral palsy. (bvsalud.org)
Pathogenic germline sequence variants in two major susceptibility genes BRCA1 and BRCA2 confer a high relative risk and explain a proportion of familial breast cancer. (lu.se)
Few other high-risk genes are known and current knowledge supports a polygenic model, a role of common low-risk variants that may interact in multiplicative fashion, but also of rare intermediate-risk gene variants. (lu.se)

The results showed that nine ZmCAMTA genes showed highly diversified gene structures and tissue-specific expression patterns. (frontiersin.org)
Analysis of Rho mRNA expression patterns in mouse tissues shows that recent subfamilies have tissue -specific and low-level expression that supports their implication only in narrow time windows or in differentiated metabolic functions. (xenbase.org)
We now have identified and characterized 54 miRNAs from rainbow trout somatic tissues and profiled their expression patterns. (usda.gov)
Real-time PCR was used to measure miRNA expression patterns in adult somatic tissues and unfertilized eggs. (usda.gov)
The majority of the miRNAs showed characteristic tissue-specific expression patterns suggesting potential roles in maintaining tissue identity. (usda.gov)
Quantitative real-time polymerase chain reaction analysis identified that expression patterns of bZIP s differed, including in different organs and under various abiotic stresses. (biomedcentral.com)
Breast tumors can be classified into subtypes based on patterns of gene expression, DNA methylation, nucleotide substitutions and genomic rearrangements. (lu.se)
Strong selection pressures experienced during one stage of development may differ from those experienced in other stages, and with consequences for the underlying patterns of gene expression. (lu.se)
We want to understand differences in life stage-specific gene expression in the peacock fly and relate these patterns to signatures of selection across the genome. (lu.se)

One of the methods that does seem to work well is TargetScan, which relies on both pairing of seed sequences (a subset of the 18-23 bp that make up a miRNA) and phylogenetic conservation of sites. (lu.se)
High-throughput methods for assessment of function are clearly required if this wealth of primary sequence information is to be used. (medscape.com)

In vertebrates, gene duplications and retrotranspositions increased the size of each chordate Rho subfamily, whereas RhoH , the last subfamily, arose probably by horizontal gene transfer. (xenbase.org)
These genomes will be compared to all other available genomes, and machine learning models that account for duplications and genome quality will be developed to estimate the fitness consequence of every base in the genome. (usda.gov)

Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.com)
This will include co-expression network analyses to identify groups of genes that are expressed similarly and might belong to the same or linked gene regulatory networks. (lu.se)

and rapidly determine all the DNA sequences in the genome that regulate the expression of a specific gene. (finchannel.com)

The amount of actual nucleotide sequence in the latest version of the reference genome ( GRCh38.p13 ) is 3,110,748,599 bp and the estimated total size is 3,272,116,950 bp based on estimating the size of the remaining gaps. (blogspot.com)

MiRNAs are most often identified through computational prediction from genome sequences. (usda.gov)

Background: MicroRNAs (miRNA) are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. (usda.gov)
The rainbow trout genome sequence is not available yet, which does not allow miRNA prediction for this species which is of great economic interest for aquaculture and sport fisheries, and is a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. (usda.gov)
qRT-PCR was used to detect the expression of miRNA-149 and FOXC1 in gastric cancer tissues and cells. (hindawi.com)
Several studies have confirmed that miRNA can be used as an oncogene or tumor suppressor gene to regulate the occurrence and development of gastric cancer [ 6 ]. (hindawi.com)
miR-149 is a type of miRNA, which can regulate the biological functions of tumors by targeting multiple genes, such as TGF- β 2, GIT1, and HDAC4 [ 7 - 9 ]. (hindawi.com)
Basically, if miRNA repression is evolutionarily important for a gene, we expect the miRNA binding sites to be shared across closely related species. (lu.se)
There may be scope for future work comparing miRNA expression in different tissues between hybrids and parental species. (lu.se)

RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. (nature.com)
For decades, scientists have known that, despite its name, "junk DNA" in fact plays a critical role: While the coding genes provide blueprints for building proteins, which direct most of the body's functions, some of the noncoding sections of the genome, including regions previously dismissed as "junk," seem to turn up or down the expression of those genes. (stanford.edu)
But it's been unclear how certain noncoding regions influence gene-expression levels - that is, the number of times a gene is copied into RNA and used to make proteins. (stanford.edu)
One isolate, PBCV-1, for example, (genome size = 330744 bp dsDNA) codes for ~375 proteins, nearly half of which resemble proteins of known function. (uml.edu)
Chromosome 12 likely contains 1,100 to 1,200 genes that provide instructions for making proteins. (medlineplus.gov)

BACKGROUND: Pathogenic variation of the MECP2 gene presents mostly as Rett syndrome in females and is extremely rare in males. (bvsalud.org)

Genomic structure and assignment of the RhoH/TTF small GTPase gene (ARHH) to 4p13 by in situ hybridization. (xenbase.org)
We validated laminar patterning in each block using RNAscope in situ hybridization with Layer I and VI marker genes (RELN and NR4A2). (speakerdeck.com)
Both technologies use hybridization of labeled nucleic acid transcripts to measure the gene expression. (medscape.com)

draft genomes are not included, nor are organelle only sequences. (wikipedia.org)
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)

in cases of non-kinesiogenic dyskinesia, a mutation in the MR1 gene is detected. (bvsalud.org)
Most male patients with MECP2 gene mutation show MECP2 duplication syndrome. (bvsalud.org)
When the ETV6 - PDGFRB fusion gene mutation occurs in cells that develop into blood cells, the growth of eosinophils (and occasionally other white blood cells, such as neutrophils and mast cells) is poorly controlled, leading to PDGFRB -associated chronic eosinophilic leukemia. (medlineplus.gov)

Thirty public sector research groups across the country are part of the U.S. Genomes to Field Genotype by Environment experiment to understand how maize genetics interacts with its environment. (usda.gov)
To explore the genetics of these and other fly features, the researchers sequenced pooled genomic DNA from six adult female house flies belonging to an inbred strain called aabys. (genomeweb.com)
In: Organelle Genetics 2012, Part 2: evolution of organelle genomes and gene expression (C. Bullerwell, ed), Springer-Verlag Heidelberg, Germany, p. 41-77. (umontreal.ca)

Epigenetics involves biological processes such as DNA methylation or histone modification that do not change the genome sequence but alter gene expression. (cdc.gov)
Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. (sens.org)
Multi-walled carbon nanotube s elicit concordant changes in DNA methylation and gene expression following long-term pulmonary exposure in mice. (cdc.gov)

Using these reads we performed gene expression quantification. (biomedcentral.com)
Jain and colleagues also report that they are able to get much longer reads than has been possible with the typical Illumina sequencer, which is most commonly used for sequencing projects. (medscape.com)
Instead of getting 10 kb of sequence per read, the international team was able to get 100- to 300-kb reads. (medscape.com)
Those ultralong reads mean scientists can see parts of the genome in ways they have not before. (medscape.com)
If a repetitive region is significantly longer than the length of the typical read, it's hard to concatenate those reads into a complete sequence. (blogspot.com)
This has been particularly difficult in centromeric regions but with the development of long sequence reads this problem has been overcome. (blogspot.com)
CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads. (cdc.gov)
A confocal scanner then reads the fluorescent intensity of each hybridized sequence in the array. (medscape.com)
Sequencing is performed on NovaSeq 6000, with read structure of 2 x 150 bp and aiming for 25M reads per sample. (lu.se)

E. A. van Strien, D. Zuidema, R.W. Goldbach, Vlak, J. M. (1992) Nucleotide sequence and transcriptional analysis of the polyhedrin gene of Spodoptera exigua nuclear polyhedrosis vi-rus. (scirp.org)

Now, researchers at the University of Helsinki have, together with their collaborators at the Helsinki University Hospital, developed a new sequencing-based approach for pathogen discovery from challenging samples. (helsinki.fi)
Complete genomic sequences of microbial pathogens and hosts offer sophisticated new strategies for studying host-pathogen interactions. (medscape.com)
Host profiling might also identify gene expression signatures unique for each pathogen, thus providing a novel tool for diagnosis, prognosis, and clinical management of infectious disease. (medscape.com)

Changes to short, repetitive sequences in the genome have been linked to diseases like autism and schizophrenia. (stanford.edu)
Starting in the 1980s, researchers noticed that changes to these repetitive sequences can affect gene expression," said the study's lead author, Connor Horton, who was a technician in Fordyce's lab. (stanford.edu)
As I understand it the 5% that is remaining as unsequenced gaps are difficult to sequence primarily because they're highly repetitive in nature, is that correct? (blogspot.com)
If so, can you say more about why sequencing repetitive DNA is technically challenging? (blogspot.com)
Highly repetitive regions are unstable in plasmid/cosmids/BACs so their length and sequences couldn't be accurately determined. (blogspot.com)
In addition, it's difficult to sequence highly repetitive DNA because of stuttering and stammering during the DNA polymerase reaction. (blogspot.com)

Quantitative real-time PCR was used to test the expression of ZmCAMTA genes under several abiotic stresses (drought, salt, and cold), various stress-related hormones [abscisic acid, auxin, salicylic acid (SA), and jasmonic acid] and biotic stress [rice black-streaked dwarf virus (RBSDV) infection]. (frontiersin.org)
The expression of most ZmCAMTA genes responded to both abiotic and biotic stresses. (frontiersin.org)

To discover how the arachnid developed this ability, González, Gainett and their fellow researchers sequenced the daddy longlegs' genome - and eventually, they succeeded in creating a daddy shortlegs, by manipulating its genes. (npr.org)
Rather than trying to turn a gene off entirely, the researchers wanted to turn it down to a very low setting. (npr.org)
When the researchers turned down the expression of two specific genes, the daddy longlegs developed much shorter legs than usual. (npr.org)
Working with Addgene, Broad Institute has shared CRISPR genome-editing reagents with researchers at more than 3,200 institutions in 76 countries. (broadinstitute.org)
A study led by researchers at Stanford Medicine have unraveled some of the mystery of how non-coding DNA changes the level of gene expression. (stanford.edu)
Researchers have spent a lot of time characterizing these transcription factors and figuring out which sequences - called motifs - they like to bind to the most," Fordyce said. (stanford.edu)
To better understand the role of short tandem repeats in gene expression, the researchers stripped the mechanisms down to their basics: transcription factors and naked DNA. (stanford.edu)
Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. (medlineplus.gov)

The best average estimate was 3,286 Gb based on the sequence of 22 autosomes, one X chromosome, and one Y chromosome (Morton 1991). (blogspot.com)
Twenty-two of the pairs, chromosome numbers 1 to 22, the autosomes, are normally homologous (identical in size, shape, and position and number of genes). (msdmanuals.com)
the smaller Y chromosome carries genes that initiate male sex differentiation, as well as a few other genes. (msdmanuals.com)
The genes that occupy the same locus on each chromosome of a pair (one inherited from the mother and one from the father) are called alleles. (msdmanuals.com)
A chromosome contains many genes. (msdmanuals.com)
These cells have a total of four copies of all the genes on the p arm of chromosome 12. (medlineplus.gov)
The most common translocation that causes this condition fuses part of the PDGFRB gene from chromosome 5 with part of the ETV6 gene from chromosome 12, written as t(5;12)(q31-33;p13). (medlineplus.gov)

Generation of BALB-MuSV and Ha-MuSC by type C virus transduction of homologous transforming genes from different species. (xenbase.org)
The technology has also made it possible to identify microbiota components up to species- and gene-level. (helsinki.fi)
We further studied the collinearity between these genes and related genes of six other species. (biomedcentral.com)

Expression of Shiga toxin 1 ( stx1 ) and stx2 genes was determined for selected isolates ( Technical Appendix ). (cdc.gov)
The genomes of other chlorella virus isolates are probably co-linear with PBCV-1 and appear to share many, but not all, genes. (uml.edu)

Sequencing Ebola and Marburg viruses genomes using microarrays. (cdc.gov)

The scanner that records the intensity value is linked to digital image analysis software, which produces a color-coded image of the array, and a quantitative value is recorded for each target gene. (medscape.com)

Nucleus-specific expression in the multinuclear mushroom-forming fungus reveals different nuclear regulatory programs. (broadinstitute.org)
M. D. Ayres, S. C. Howard, J. Kuzio, M. Lopez-Ferber, Possee R.D. (1994) The complete DNA sequence of Auto-grapha californica nuclear polyhedrosis virus. (scirp.org)
R. D. Possee, S. C. Howard, (1987) Analysis of the polyhedrin gene promoter of the Autographa californica nuclear polyhedro-sis virus. (scirp.org)
Nuclear genome sequence and gene expression of an intracellular fungal endophyte stimulating the growth of cranberry plants. (umontreal.ca)

Upon depletion of RBPJ using CRISPR/Cas9, we observed specific upregulation of Notch target gene expression. (mdpi.com)

claiming that two homologous chromosomes paired between complementary sequences lead to the formation of a cross-stranded structure that physically links the two component helices. (iucr.org)
Each gene has a specific location (locus), which is typically the same on each of the 2 homologous chromosomes. (msdmanuals.com)

Because the locations of the probes are known, the intensity and pattern of the labeled mRNA can be used to measure the expression of the targeted gene. (medscape.com)
Our RNA service includes mRNA and total RNA library preparation and sequencing on Illumina platforms. (lu.se)

L. H. Robert, Bonning B.C. (2003) Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedroviruses Journal of General Virology 84, 1827-1842. (scirp.org)
The limitations and possibilities associated with expression profiling in intracellular amastigotes and promastigotes were assessed through a series of comparative experiments in which technical and biological parameters were scrutinized. (cambridge.org)

But maleness can also be achieved by tucking the M factor sequence away in one of the house fly's five autosomal chromosomes, too - and the sex determination has undergone even more subtle tweaks in various fly populations, the study's authors explained. (genomeweb.com)
Genes are contained in chromosomes in the cell nucleus and mitochondria. (msdmanuals.com)
The 23rd pair, the sex chromosomes (X and Y), determines a person's sex as well as containing other functional genes. (msdmanuals.com)
Genes are arranged linearly along the DNA of chromosomes. (msdmanuals.com)
Some genes occur in multiple copies that may be next to each other or in different locations in the same or different chromosomes. (msdmanuals.com)

assay as gene expression input. (github.com)
After initial investment on sequencing machine and assay validation, the per gene cost of a next-gen sequencing test is much lower than Sanger-based single gene test, and we also anticipate faster turnaround time, because much of the process can be automated. (aacc.org)
Microarrays may be used to assay gene expression within a single sample or to compare gene expression in 2 different cell types or tissue samples, such as in healthy versus diseased tissue. (medscape.com)

Similarly, in specific cases, such as cancers, viral infections and in certain cell-types during normal development, mutations and other structural variations within the genome also influences cellular functions. (confex.com)
My graduate and postdoctoral research has focused on investigating how the genome and epigenome regulates the dynamics of gene expression in viral and mammalian systems 8 . (confex.com)

It possesses a unique forkhead domain combined with a fragment of the target gene to initiate transcription [ 10 ] and regulates various biological processes such as tumor cell differentiation, cell proliferation, and migration [ 11 ]. (hindawi.com)

The GeneRIF (Gene References into Function) directory contains PubMed identifiers for articles describing the function of a single gene or interactions between products of two genes. (nih.gov)

MicroRNAs (miRNAs) are noncoding RNAs of approximately 22 nucleotides, which are key regulators of gene expression [ 4 ]. (hindawi.com)
miRNAs are small noncoding RNAs that have broad regulatory functions on gene expression. (lu.se)

Assembly of the alignments into full transcripts and quantification of the expression levels of each gene/transcript. (lu.se)

Many patients can undergo DNA testing now with next-gen sequencing while they were not appropriate for conventional sequencing, because doctors did not have a reasonable clinical diagnosis for them and we did not know which gene to test for for Sanger sequencing. (aacc.org)
So next-gen can now offer answers for patients without a clear clinical diagnosis, and that has opened doors for more patients that were previously not suitable for DNA test sequencing. (aacc.org)

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

Important regulatory factors, TFs bind to the promoter regions of target genes and activate or inhibit their transcription. (biomedcentral.com)

It is the only mushroom-forming fungus for which genes have been inactivated by homologous recombination. (nature.com)

Anatomy15

Organisms24

Diseases2

Chemicals and Drugs45

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Phenomena and Processes137

Disciplines and Occupations6

Technology, Industry, Agriculture2

Information Science13

Health Care5

Geographicals1

Transcriptome8

Genetic22

Microarray6

Genomics8

Characterization6

Regulation4

Protein23

Bioinformatics1

Data26

Encode2

Mitochondrial7

Biology4

Molecular8

Annotation4

Pathways2

Differentially1

Bacterial2

Epigenetic3

Identification4

Human16

Variants5

Patterns9

Methods2

Duplications2

Analyses2

Regulate the expression1

Reference genome1

Computational1

MiRNA7

Proteins5

Pathogenic1

Hybridization3

Draft2

Mutation3

Genetics3

Methylation3

Reads9

Nucleotide1

Pathogen3

Repetitive6

Abiotic2

Researchers8

Chromosome7

Species3

Isolates2

Ebola1

Quantitative1

Nuclear4

CRISPR1

Homologous chromosomes2

MRNA2

Comparative2

Chromosomes5

Assay3

Viral2

Regulates1

Interactions1

RNAs2

Quantification1

Clinical2

Cancers1

Target genes1

Mushroom-formin1