Complement transcriptome proteins expressed sequence tags. Medical search. Frequent questions

Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. (wikipedia.org)
Preliminary analyses using 454 transcriptome and Bacterial Artificial Chromosome (BAC) sequences from three Heliconius species highlighted a cluster of genes within each region showing relatively higher rates of sequence evolution. (biomedcentral.com)
A combination of de novo transcriptome assembly and DGE analysis was shown to be a powerful method for identifying genes encoding enzymes potentially involved in the biosynthesis of important secondary metabolites in a non-model plant. (biomedcentral.com)
We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. (frontiersin.org)
With 35,000 genes and hundreds of thousands of protein states to identify, correlate, and understand, it no longer suffices to rely on studies of one gene, gene product, or process at a time. (genomicglossaries.com)
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)
ACC) Unsupervised consensus clustering recognized two self-employed subclusters based on the manifestation levels of the differentially expressed genes between two cell claims spanning the longest pseudotime. (biotech2012.org)
Moreover, trajectory analysis exposed that myeloid cells evolutionarily consisted of 7 claims, and antigen-presenting molecules and complement-associated genes were lost along the pseudotime circulation. (biotech2012.org)
Poor clinical outcome was correlated with elevated HIF-1α and podoplanin expression whilst expression of inflammatory and complement genes was predictive of extended survival. (elifesciences.org)
One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune . (nature.com)
By transcriptome analyses (RNA-seq and RT-PCR) we confirm these observations as PilG is shown to upregulate many genes involved chemotaxis and flagellar biosynthesis but these similar genes were downregulated by PilH. (biomedcentral.com)
Taken together, we demonstrate that for the conditions tested PilG and PilH have inverse regulatory effects on flagellum-dependent and pili-dependent motility in Xcc and that this regulatory impact depends on these proteins influences on genes/proteins involved in flagellar biosynthesis and pilus assembly. (biomedcentral.com)
2 3 The HGP demonstrated that a relatively limited number of genes could be identified in the human genome, which substantiated the theory that complex biological processes were regulated on other levels than DNA sequence alone. (bmj.com)
describe a novel method to identify potential transcription factors from a list of differentially expressed genes using textual similarity between the genes and transcription factors reported in the literature [ 30 ]. (biomedcentral.com)
Importantly, their approach has the potential to identify transcription factors that might be indirectly regulating the genes and, thus, would not be recognized by sequence-based analysis of the expressed gene promoters. (biomedcentral.com)
The researchers measured relative protein levels from over 12,000 genes across 32 normal human tissues. (ddw-online.com)
Biomphalaria glabrata transcriptome: identifi-cation of cell-signalling, transcriptional control and immune-related genes from open reading frame expressed sequence tags (ORESTES). (ac.ir)
Commonly used gene expression profiling tools are sub-optimal for the study of lung tissue as they focus on well-characterized genes, resulting in the omission of a significant amount of information potentially of biological importance within the lung transcriptome. (biomedcentral.com)
Comparative analysis of these pathways relies on network alignment methods, much the same way as sequence matching and alignments are used for individual genes and proteins. (biomedcentral.com)
Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. (biomedcentral.com)
Our studies suggest that the ascidians contain the basic ancestral complement of vertebrate GPCR genes. (biomedcentral.com)
This is evident at the subfamily level comparisons since Ciona GPCR sequences are significantly analogous to vertebrate GPCR subfamilies even while exhibiting Ciona specific genes. (biomedcentral.com)
Eleven candidate reference genes were identified from the transcriptome data. (mpob.gov.my)

Biotin-ubiquitin tagging of mammalian proteins in Escherichia coli. (nih.gov)
Glycosylation refers to a sequence of events that take place in the Golgi body and the endoplasmic reticulum of the cells of the expression system (predominantly mammalian) that lead to post-translational addition and processing of carbohydrate or glycan moieties to the protein backbone (usually serine- or threonineâ linked glycosylation for O-linked glycans and asparagineâ linked glycosylation for N-linked glycans) (6). (chromatographyonline.com)
The mammalian transcriptome has been estimated to consist of as many as 10 7 RNAs [ 23 ] and it has been suggested that the transcript rather than the gene should be regarded as the operational unit of the genome [ 24 ]. (biomedcentral.com)

Phylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: (1) Appendicularia, (2) Thaliacea + Phlebobranchia + Aplousobranchia, (3) Molgulidae, and (4) Styelidae + Pyuridae. (biomedcentral.com)
Global transcriptome and chromatin occupancy analyses of ZNF148 revealed a central role in inhibiting cancer cell de-differentiation and migration. (nature.com)
Co-immunoprecipitation, bacterial two-hybrid and pull-down analyses showed that PilH and PilG were able to interact with district subsets of proteins that potentially account for their regulatory impact. (biomedcentral.com)
The phylogenetics, functional domain and protein-protein interaction analyses suggest an immunological role for Bg TEP in B. glabrata . (ac.ir)

Genomic and cDNA sequence alignments as well as chromosome localization using nullisomic-tetrasomic lines provided strong evidence for three expressed gene copies located on homoeolog chromosomes for TaSK1 as well as for TaSK2 . (biomedcentral.com)
We divide the field of genomics into genotyping (focused on the genome sequence), transcriptomics (focused on genomic expression) and epigenomics (focused on epigenetic regulation of genome expression). (bmj.com)
Genomic sequences of TEPs were retrieved after annotation of the B. glabrata genome. (ac.ir)
Once dismissed as "junk" genomic material, non-protein-coding DNA is now appraised more highly. (pharmaceuticalintelligence.com)
In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research. (peerj.com)

Isoliquiritigenin Methods: A single-cell RNA sequencing (scRNA-seq) dataset and seven PDAC cohorts with total clinical and bulk sequencing data Isoliquiritigenin were collected for bioinformatics analysis. (biotech2012.org)
Here, we combine spatial transcriptomics and scRNA-Seq datasets to define the transcriptome of tumor-proximal and tumor-distal cancer-associated fibroblasts (CAFs) and link this to clinical outcome. (elifesciences.org)
Additionally, single-cell RNA sequencing (scRNA-seq) analysis was performed for anti-S B lymphocytes obtained from four donor individuals 210.0 days post-second dose and 10.0 days post-third dose of Comirnaty vaccines. (news-medical.net)

Methods Sources of Datasets A single-cell sequencing dataset ("type":"entrez-geo","attrs":"text":"GSE155698″,"term_id":"155698″,"extlink":"1″GSE155698) including 16 PDAC and 3 adjacent normal samples was from the Gene Manifestation Omnibus (GEO). (biotech2012.org)
By combining the two datasets, the software carries out the unique sequence tag identification, tag counting for transcript quantification, and cross-platform sequence matching functions, whereby the short sequence tags can be annotated with a function, level of expression, and Gene Ontology (GO) classification. (biomedcentral.com)
Bookend is a generalized framework that utilizes RNA 5′ and 3′ end information in RNA-seq datasets to accurately reconstruct transcriptomes including those from single cells. (biomedcentral.com)

RNA viruses may escape acquired humoral and cellular immune responses by mutations in protective antigenic epitopes (e.g., avian influenza viruses), while accessory nonstructural proteins or multifunctional structural proteins interfere with the interferon system (e.g. (imperial.ac.uk)

Multiple transcript variants encoding two different isoforms were identified through sequence analysis. (wikipedia.org)
To understand how transcriptome architecture varies during development and in response to disease, it is therefore valuable to have an automated method that accurately identifies transcript isoforms. (biomedcentral.com)
Long-read methods are a promising tool for transcript annotation, but current protocols are more error-prone per base sequenced, less sensitive, and more costly than comparable short-read experiments. (biomedcentral.com)

Recent studies indicated that digital gene expression profiling based on short sequence tags has superior performance as compared to other transcriptome analysis platforms including microarrays. (biomedcentral.com)
The combination of different next generation sequencing techniques like 454 pyrosequencing and Illumina Genome Analyzer (Solexa) will enable high-throughput and accurate global gene expression profiling in species with limited genome information. (biomedcentral.com)
A combination of large-scale in-house sequencing, gene expression profiling and public sequence and gene expression data mining were used to characterise the transcriptome of NSCLC and the data used to generate a disease-focused microarray - the Lung Cancer DSA research tool. (biomedcentral.com)
Therefore, focusing on the generation of gene expression arrays comprehensively representing the transcriptomes of individual tissues and diseases is a more feasible approach with current technology platforms. (biomedcentral.com)

The OMICS field ranges from genomics (focused on the genome) to proteomics (focused on large sets of proteins, the proteome) and metabolomics (focused on large sets of small molecules, the metabolome). (bmj.com)
The B. glabrata genome contains 14190 unannotated proteins after filtration with about 85% of its proteome annotated. (ac.ir)

The use of tag-based methods in species without genome sequence should be complemented by other methods such as cDNA library sequencing. (biomedcentral.com)

Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. (wikipedia.org)

Considering that each microRNA regulates up to hundreds of different mRNAs, and that each mRNA is regulated by tens of microRNAs, this finding adds a new layer of complexity to the regulatory dynamics of the human transcriptome. (pharmaceuticalintelligence.com)
However, once deep sequencing became widely available, microRNA variants that showed differences at their 5′- or 3′-termini have been described. (pharmaceuticalintelligence.com)

One of the unexpected findings of the Human Genome Project was that over 98% of the human genome does not encode for proteins. (pharmaceuticalintelligence.com)

CITE (cellular indexing of transcriptomes and epitopes)-sequencing was performed for labeling anti-S and anti-S RBD (receptor-binding domain)-binding B lymphocytes. (news-medical.net)

Proteomics, the large-scale study of proteins, is holding increasing significance and opportunity as we look to find treatments for a range of conditions such cancer, fatty liver disease and diabetes. (ddw-online.com)
According to Lihua Jiang, a proteomics expert in the Snyder Laboratory responsible for proteomics profiling of host samples of the project, "the tissue-specific distribution of proteins can provide an in-depth view of complex biological processes that require the interplay of multiple organs. (ddw-online.com)

RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. (frontiersin.org)
To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. (biomedcentral.com)
By sequence similarity analysis and functional assays from the species Streptomyces lividans TK23, S. coelicolor A3(2) and S. glaucescens GLA.O, first hints for a widespread lack of MalP and presence of AmlE in the class Actinobacteria were given. (frontiersin.org)
CPTRA is a powerful software package for next generation sequencing-based transcriptome profiling in species with limited genome information. (biomedcentral.com)
According to our case study, the strategy can greatly broaden the application of the next generation sequencing for transcriptome analysis in species without reference genome sequence. (biomedcentral.com)
Considering the read length, 454 sequencing has some advantages for transcriptome analysis, since the longer reads allow for better assembly of the sequences, which is particularly important for species without reference genome information. (biomedcentral.com)
J. Pinzon and T. Lajeunesse , Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology , Molecular Ecology , vol. 37 , issue. (hal.science)

Many complex disorders are driven by a coupling of housekeeping (universally expressed in all tissues) and tissue-selective (expressed only in specific tissues) dysregulated pathways. (biomedcentral.com)
While 50-60% of the microRNAs previously deposited into the miRBase are expressed in multiple tissues, only about 10% of the newly discovered microRNAs are shared across multiple tissue types. (pharmaceuticalintelligence.com)

This approach serves as a template for the development of other disease transcriptome microarrays, including non-neoplastic diseases. (biomedcentral.com)

Aided by state-of-the-art, high-throughput computational methods, the current study simulated and analyzed the dynamics of competitive histamine binding at the tick-host interface using the available crystal structures of both the tick salivary lipocalin histamine-binding protein from Rhipicephalus appendiculatus and the human histamine receptor 1. (biomedcentral.com)

Participants also had the opportunity to attend hands-on workshops on NCBI tools, presented by Peter Cooper from NCBI/NIH, and on protein evolution, presented by Hugh Nicholas and Troy Wymore, from the Pittsburgh Supercomputing Center. (biomedcentral.com)
In addition, TEP sequences deposited in NCBI protein database were also retrieved and utilized for sequence analysis. (ac.ir)

However, the transcriptomic analysis with tag-based methods often depends on available genome sequence. (biomedcentral.com)
The combination of transcriptome data acquisition methods requires cross-platform transcriptome data analysis platforms, including a new software package for data processing. (biomedcentral.com)
C ross- P latform TR anscriptome A nalysis, to analyze transcriptome profiling data from separate methods. (biomedcentral.com)
These methods have been previously applied to detection of ortholog proteins, projection of functional pathways, and construction of phylogenetic trees. (biomedcentral.com)

In contrast, inflammatory CAFs were dominant within tumor-distal subsets and expressed complement components and the Wnt-inhibitor SFRP2. (elifesciences.org)

These results do not support a major role for transcriptional transitions in the time of onset of DNA methylation in the oocyte, but suggest a model in which sequences least dependent on chromatin remodelling are the earliest to become permissive for methylation. (biomedcentral.com)

G protein-coupled receptors (GPCRs) constitute a large family of integral transmembrane receptor proteins that play a central role in signal transduction in eukaryotes. (biomedcentral.com)

For the software, the input data included a long-read sequence dataset with proper annotation, and a short-read sequence tag dataset for the quantification of transcripts. (biomedcentral.com)

To date, molecular dynamics simulations focus on protein-protein and protein-ligand interactions, but there are currently no studies for simultaneous ligand exploration between two competing proteins. (biomedcentral.com)
Three explanatory types of data can be obtained from the current study: (i) the dynamics of multiple binding sites, (ii) competition between two proteins for a ligand, and (iii) the intrinsic molecular components involved in the competition. (biomedcentral.com)
Tumor-proximal fibroblasts comprise large populations of myofibroblasts, strongly expressed podoplanin, and were enriched for Wnt ligand signaling. (elifesciences.org)
These moieties are critical in terms of their role in in-vivo safety and efficacy (pharmacodynamics and pharmacokinetics), protein folding, protein targeting and trafficking, ligand binding, stability, protein halfâ life regulation, and immunogenicity (8). (chromatographyonline.com)

The diversity among GPCRs primarily stem from the presence of characteristic N-terminal extracellular domains and C-terminal intracellular domains and to a relatively lesser extent from the connecting loops which share limited sequence similarity. (biomedcentral.com)

Abstract Background: The treatment modalities for pancreatic ductal adenocarcinoma (PDAC) are limited and Mouse Monoclonal to MBP tag unsatisfactory. (biotech2012.org)

Or to be more precise, at least some portions of non-protein-coding DNA are thought to serve important biological functions. (pharmaceuticalintelligence.com)
Non-natural oligonucleotides are valuable probes of biological systems, as they can convey synthetic control of endogenous nucleic acids with high sequence specificity. (cdc.gov)

Advancements in bioinformatics has significantly supported RNA-Seq technology to accelerate the knowledge on transcriptomes ( 1 ). (frontiersin.org)
while John Weinstein, Chair of the Department of Bioinformatics and Computational Biology at the University of Texas M.D. Anderson Cancer Center, talked on "Personalizing Cancer Medicine in the Era of Next-Generation Sequencing: Omics and Informatics. (biomedcentral.com)

The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the capsule extract from Uncaria , and provides information that may aid in metabolic engineering to increase yields of these important alkaloids. (biomedcentral.com)
The DEGs were also typed into protein-protein interaction (PPI) networks to get the interaction data. (medscimonit.com)
However, maximizing the potential for next generation sequencing heavily depends on available data analysis tools [ 1 ]. (biomedcentral.com)
Some features of next generation sequencing data are different from those of traditional Sanger sequencing. (biomedcentral.com)
The different sequence formats, diverse applications, and the large amount of data generated all require new strategies for sequence analysis [ 1 ]. (biomedcentral.com)
Tissue-specific proteins were identified and compared to RNA data. (ddw-online.com)
Using Argonaute CLIP-seq data, Dr. Rigoutsos and colleagues showed that similar percentages of the two sets of microRNAs were in complex with Argonaute proteins. (pharmaceuticalintelligence.com)

Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. (peerj.com)
Accordingly, many computational tools have been developed for genome annotation including software that utilizes the massive and growing diversity of RNA sequencing (RNA-seq) technologies [ 12 ]. (biomedcentral.com)

Single-cell RNA sequencing was performed to obtain transcriptomic profiles. (biomedcentral.com)

The 454 pyrosequencing platform provides a longer read lengths of 200 to 400 bases and relatively less sequencing yield at around 200 to 400 megabases per run [ 18 ]. (biomedcentral.com)

During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. (biomedcentral.com)

Like most bacteria, Xcc uses a variety of extracellular protein structures to interact with their surrounding environment and drives cellular movement. (biomedcentral.com)
These extracellular protein structures called flagella and pili contribute cellular movement in the form of 'swimming' and 'swarming', respectively. (biomedcentral.com)
At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. (stanford.edu)

A collection of different allotypes or allelic protein variants, a new type of protein library. (genomicglossaries.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)

Bg TEP relatedness to its other homologues as well as functional domain and protein-protein interaction analysis was performed. (ac.ir)

propose a one-dimensional diffusion-reaction model, in the form of a master equation, to analyze the non-equilibrium protein sliding kinetics along a segment of bacterial DNA [ 29 ]. (biomedcentral.com)

There is paucity of information on functional relationship and characterization of Biomphalaria glabrata thioester-containing proteins ( Bg TEP) to other well-annotated homologues. (ac.ir)

Among these tick salivary proteins are lipocalins, antiparallel beta-barrel proteins that sequester small molecules. (biomedcentral.com)
The crystal structure of one of these tick salivary Ra-HBPs (Ra-HBP2) revealed a few structural deviations from the archetypal lipocalin protein family, that it sequesters two histamine molecules, and also causes an inhibition of guinea-pig ileum to contract by competing with H1R/H2R for histamine binding [ 6 ]. (biomedcentral.com)

Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. (frontiersin.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)

Hunting highlighted how researchers in the lab of Michael Snyder, Stanford B. Ascherman Professor and Chair of Genetics and Director of Genomics and Personalized Medicine at Stanford University School of Medicine, generated the most comprehensive protein map to date. (ddw-online.com)

We believe that this platform enables comprehensive transcriptome level expression profiling of lung tissue samples. (biomedcentral.com)

Salivary gland transcriptomes have revealed that ticks, as obligate hematophagous (blood feeding) arthropods, secrete many protein families at the injury site to counteract host physiological responses - antagonizing inflammation is one example of the mechanisms ticks employ. (biomedcentral.com)

Ticks counteract host inflammatory responses by secreting proteins from their saliva that compete for histamine binding. (biomedcentral.com)

Among them, CD8+ T cells and NKT cells were universally worn out by expressing exhaustion-associated molecular markers. (biotech2012.org)

The map shows where proteins are expressed throughout the human body, providing new insights into regulation, secretome, metabolism, and human diseases. (ddw-online.com)
Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. (elifesciences.org)
Purification of individual SARS-CoV-2 proteins from human cells have identified a potential interaction between a catalytic-inactive version of Nsp5 with human tRNA methyltransferase 1 (TRMT1) ( Gordon et al , 2020b ). (elifesciences.org)
This complexity is primarily due to processes such as the alternative splicing and polyadenylation of coding transcripts and the presence of non-coding and antisense transcripts, with non-coding transcripts thought to make up a substantial proportion of the human transcriptome [ 21 , 22 ]. (biomedcentral.com)

Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. (biomedcentral.com)

Predicted to be involved in positive regulation of protein sumoylation and protein sumoylation. (nih.gov)

We envisioned that enzyme-activatable cMOs could overcome these limitations, as the triggering enzymes could be expressed in individual cell populations using cis regulatory elements. (cdc.gov)

Extracts containing these terpene indole alkaloids (TIAs) can inhibit the formation and destabilize preformed fibrils of amyloid β protein (a pathological marker of Alzheimer's disease), and have been shown to improve the cognitive function of mice with Alzheimer-like symptoms. (biomedcentral.com)
The trapping sites were innovatively positioned to represent a large grid and mice were electronically tagged so researchers could keep precise track of where the animals were being recaptured. (vetscite.org)
Retinas were treated with IL1β prior to NMDA damage and cell death was assessed in wild type, IL-1R1 null mice, and mice expressing IL-1R1 only in astrocytes. (biomedcentral.com)

Co-dominant simple sequence repeat (SSRs) are popular DNA markers, widely applied in oil palm genetic studies, especially in genetic mapping, marker-trait association, diversity analysis and detecting illegitimacy. (mpob.gov.my)

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