Sentences with phrase «gene transcripts in»

Not exact matches

Based on the transcript sequences, the researchers identified 1,437 new promoters — short DNA sequences where transcription begins — in or between genes, on top of the 1,730 promoters they knew of.

Transcripts from 65 percent of the genes incorporate pieces of DNA from relatively far outside of the genes or even from one or two other genes, says molecular biologist and consortium member Tom Gingeras of Affymetrix, a genome technology company in Santa Clara, Calif..

The discovery that much of the mammalian genome is transcribed, in some places without gaps (so - called transcriptional «forests»), shines a bright light on this embarrassing plentitude: an order of magnitude more transcripts than genes (pp. 1559, 1564, and 1529).

She bred a mouse in which the antisense transcript was «knocked down» and the paternal copy of the gene turned on.

The same agents that damage DNA also damage its sister molecule messenger RNA (mRNA), which ferries transcripts of the genes to the tens of thousands of ribosomes in each cell.

Expression of these genes appears in the blood in the form of specific RNA transcripts.

Single - cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4 - CTLs, compared with CD4 + T cells in the central memory (TCM) and effector memory (TEM) subsets.

Single - cell RNA sequencing allows researchers to determine the precise nature of the total gene transcripts, or all of the genes that are actively expressed in a particular cell.

«While previous molecular studies have provided simple snapshots of the gene transcript variations that are associated with the exposure of insects to natural and synthetic chemicals, the genomics approaches used in this study offer a significantly more complex perspective on the biochemical and physiological processes occurring in plant - insect interactions,» Schuler said.

The Neurogenomiks research group, linked to the Achucarro Basque Centre for Neuroscience (EHUgroup) and the University of the Basque Country (UPV / EHU), has just had a research article published in the scientific publication Journal of Immunology; it details how they have managed to show that the gene known as ANKRD55 produces 3 different transcripts of the messenger RNA, and that the genetic variant associated with MS greatly increases the production of these transcripts.

Gene expression patterns in the hippocampus samples were examined using DNA microarrays that measured the expression levels of over 30,000 genes (transcripts) per sample.

In a study published online in Genome Research, researchers devised a strategy for genome - wide annotation of primary miRNA transcripts, providing extensive new annotations in human and mouse, and shedding light on mechanisms of regulation of microRNA gene expressioIn a study published online in Genome Research, researchers devised a strategy for genome - wide annotation of primary miRNA transcripts, providing extensive new annotations in human and mouse, and shedding light on mechanisms of regulation of microRNA gene expressioin Genome Research, researchers devised a strategy for genome - wide annotation of primary miRNA transcripts, providing extensive new annotations in human and mouse, and shedding light on mechanisms of regulation of microRNA gene expressioin human and mouse, and shedding light on mechanisms of regulation of microRNA gene expression.

A natural process called nonsense - mediated decay, or NMD, provides cells with the ability to detect errors in the coded RNA messages, called transcripts, that are copied from DNA when genes are activated.

Importantly, 25 of the 115 transcripts, shared by EFTF - expressing pluripotent cells and the EF, encode for 15 genes that are both expressed in retinal stem / progenitor cells and required for normal eye formation in frogs, fish, mice, or humans (Figure 1C; Table S1).

In order to focus on genes that share similar biological processes and correlate with the calcification process, the analysis continued for unique up - regulated gene transcripts and total up - regulated gene transcripts that were differentially expressed during daytime (437 genes for unique and 1,333 for total), and during night - time (267 genes for unique and 1,171 for total).

Transcript abundances and raw read counts for all annotated S. viridis genes (v1) in the wild type compared with bsl1 - 1 mutant inflorescence primordia.

These targets were identified based on the presence of predicted regulator binding sites or experimental regulator binding in the target promoter, and / or changes in the target gene's transcript levels in regulator mutant strains.

This is consistent with work in other systems that showed transcripts from BR biosynthesis genes accumulated following loss of BR due to negative feedback regulation (Bancoş et al., 2002; Tanabe et al., 2005; Tanaka et al., 2005).

Imaging Real - Time Gene Expression in Living Systems with Single - Transcript Resolution: Construct Design and Imaging System Setup.

Regulation of transcript levels of the Arabidopsis cytochrome p450 genes involved in brassinosteroid biosynthesis

«This way we can link local environmental conditions to microbial gene - and transcript profiles and in the future quickly determine the environmental status of samples of unknown character».

The plan is to analyze the genes and gene - transcripts of microorganisms in the sea to determine what metabolic processes are active and from this get information on the environmental status.

By comparing the V. carteri germ and somatic cell transcriptomes, Matt and Umen found that the somatic cells had more transcripts from young, lineage - specific genes, whereas the germ cells had more transcripts from ancient genes that are similar to those expressed in stem cells from animals and land plants.

Figure 4D shows transcript levels for the endogenous NtPOR gene and the introduced AtChlase and AtRCCR genes in the transgenic control plant (NT 4.1.3) and transgenic plants exposed to TNT.

This figure depicts how the expression of the longer transcript in this gene becomes less dominant as PMI increases, and, as a consequence, the abundance of the different isoforms tends to converge

Disrupting «Silent» Genes The number of transcripts appears to exceed the number of mutable loci in several extensively analyzed segments of the Drosophila genome (34 - 35).

The authors highlight the importance of measuring the variability of transcript expression and location in so many cells by using their data to discover genes with related functions in the cell.

For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections.

That study showed a non-monotonic increase in the abundance of certain transcripts and suggested that previously silenced genes were actively transcribed at later post-mortem time points.

For the remaining genes, all genes detected at TPM > 1 in at least one of the tissues or cell lines used in the RNA - seq analysis are classified as «Evidence at transcript level».

For each gene, we report the abundance in «Transcript Per Million» (TPM) as the sum of the TPM values of all its protein - coding transcripts.

Together, these form the most complete annotation of immune - related genes in N. vitripennis to date, and represent one of the first genomic - scale annotations of novel immune - induced transcripts in Hymenoptera.

All genes in the classes «Experimental evidence at protein level» or «Experimental evidence at transcript level» are classified into the first two evidence categories, whereas genes from the «Inferred from homology», «Predicted», or «Uncertain» classes are classified as «No evidence».

To identify key molecular mediators of the ABL kinases implicated in the regulation of the ABL1 / ABL2 - dependent pathways, we analyzed the expression of individual genes for transcripts altered by loss of the ABL kinases.

Real rates of change can only be determined from actual transcript numbers, and this gives us the kinetics of gene expression which we are interested in.»

We therefore used Cufflinks to generate de novo assemblies from the sequencing reads in order to identify full length transcripts for OR and VR genes [30].

Although the genes implicated in these disorders are involved in a variety of pathways, most of them share a molecular phenotype: high (and often transcript ‐ specific) expression in retinal tissue.

Of the remaining features, about 75 % represent single - exon transcripts, leaving 756 and 847 putatively novel multi-exonic genes expressed in the VNO and OM respectively.

Our results revealed that transcript levels of temporally induced genes are highly correlated in individual cells.

OR and V1R genes typically have coding regions that span a single exon, but we identified 54 OR and 15 V1R genes where at least one of the reconstructed transcripts has an intron within the protein coding sequence (as annotated in Ensembl).

About 30 % of these putative genes have known protein domains and 80 % lie within transcripts predicted in silico.

But in a recent study, researchers described a balancing act that seems more counterintuitive than most: Bacterial cells prioritize transcription — the process of making RNA transcripts of genes as the first step in protein production — over repairing double - strand breaks in their DNA.

In 2012, Plessy et al. reported the expression of 955 OR genes using nanoCAGE, a methodology that captures the 5 ′ end of transcripts and generates short sequence reads around that region [29].

A few receptor genes have more than 8 different isoforms (38 VRs and 10 ORs), however in most of these cases this is due to the presence of several transcription start sites (TSS) or exons that differ in length by just a few nucleotides, so several of the final transcripts differ only very slightly (Figure S7B).

RNA - Seq has proven excellence in providing information about the regulation and transcript levels of genes.

Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively.

For example, cluster 5 of the concise «Time Series», which consists of transiently induced genes around day 3 of differentiation, similarly to Global Cluster 30, contains the same transcripts, but in addition, it also includes T - brachyury, Axin2, Mesp2, Fgf8, Wnt8a, Sp5, Sp8, Follistatin, Mix1 and Lim1.

Furthermore, the levels of transcripts of two AlkB genes that protect against the cytotoxicity of methylating agents through repair of the specific DNA lesions generated in single - stranded DNA, Alkhb3 (alkylation repair homolog 3) and Alkhb8 (alkylation repair homolog 8), was lower in the IVC males.

Our analysis predicts that the latter participate in the same biological processes as the known genes in the corresponding clusters — thus providing a starting point to study the function of poorly characterized transcripts.

These include: a) Global Clusters that consist of a small, tight subset of genes that are co-expressed under the entire spectrum of experimental conditions; b) Time Series of gene expression profiles during successive days of standard ES cell differentiation; c) Specific Gene Classes based on hierarchical clustering of transcriptional factors and ESTs; d) Expression Waves of genes with characteristic expression profiles during ES cell differentiation, juxtaposed to waves of genes that behave in the exact opposite way; e) Pathway Animations that illustrate dynamic changes in the components of individual KEGG signaling and metabolic pathways viewed in time - related manner; and, f) Search Engines to display the expression pattern of any transcript, or groups of transcripts, during the course of ES cell differentiation, or to query the association of candidate genes with various FunGenES database clustgene expression profiles during successive days of standard ES cell differentiation; c) Specific Gene Classes based on hierarchical clustering of transcriptional factors and ESTs; d) Expression Waves of genes with characteristic expression profiles during ES cell differentiation, juxtaposed to waves of genes that behave in the exact opposite way; e) Pathway Animations that illustrate dynamic changes in the components of individual KEGG signaling and metabolic pathways viewed in time - related manner; and, f) Search Engines to display the expression pattern of any transcript, or groups of transcripts, during the course of ES cell differentiation, or to query the association of candidate genes with various FunGenES database clustGene Classes based on hierarchical clustering of transcriptional factors and ESTs; d) Expression Waves of genes with characteristic expression profiles during ES cell differentiation, juxtaposed to waves of genes that behave in the exact opposite way; e) Pathway Animations that illustrate dynamic changes in the components of individual KEGG signaling and metabolic pathways viewed in time - related manner; and, f) Search Engines to display the expression pattern of any transcript, or groups of transcripts, during the course of ES cell differentiation, or to query the association of candidate genes with various FunGenES database clusters.