Analysis expressed sequence tags. Medical search. Frequent questions

We have shown that approximately 14% of the newly sequencedexpressed sequence tags map completely or partially to genomic regions where there are no annotated genes orsplice variants and therefore, imply that these are novel genetic structures. (sfu.ca)
Expressed sequence tags, which mapto intergenic (around 1000) and intronic regions (around 580), may represent novel transcribed regions, such asunannotated or unrecognized small protein-coding or non-protein-coding genes or splice variants. (sfu.ca)
Because these clones consist of DNA that is complementary to mRNA, the ESTs represent portions of expressed genes. (wikipedia.org)
Some authors use the term "EST" to describe genes for which little or no further information exists besides the tag. (wikipedia.org)
In this study, a suppression subtractive hybridization cDNA library approach was used for the identification of pathogen and plant genes that were differentially expressed during infection of the susceptible cultivar BRS Pérola of Phaseolus vulgaris L. A total of 979 unigenes (430 contigs and 549 singletons) were obtained and classified according to their functional categories. (frontiersin.org)
Alice: Endosperm-preferred expression of maize genes as revealed by transcriptome-wide analysis of expressed sequence tags. (embrapa.br)
Searches against the human genomic sequence and comparative genomic analysis of human and mouse genomes was carried out using basic local alignment search tools (BLAST), BLASTN, and BLASTX, for identifying protein coding genes corresponding to the ESTs. (elsevierpure.com)
Subsequently, in order to pick the most relevant candidate genes for a more detailed analysis, we looked for domains/motifs in the open reading frames using SMART and Pfam programs. (elsevierpure.com)
The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)
Moreover, 5′- and 3′-UTR sequences of 4378 genes have been retrieved and alternatively spliced variants of 69 genes have been identified. (biomedcentral.com)
We successfully employed deep sequencing RNA-Seq data in combination with an elaborate bioinformatics strategy in order to identify novel genes, incorrect gene models and mechanisms of transcript processing in the corn anthracnose fungus C. graminicola . (biomedcentral.com)
Sequence data of the revised genome annotation including several hundreds of novel transcripts, improved gene models and candidate genes for alternative splicing have been made accessible in a comprehensive database. (biomedcentral.com)
Of these unique sequences, over 35% had significant similarities to known genes by BLASTX searches, which allowed the identification of 14,776 unique genes in the catfish. (auburn.edu)
Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (nih.gov)
Targeted integration by homologous recombination enables in-situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum . (umontreal.ca)
using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. (biomedcentral.com)
Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. (biomedcentral.com)
Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (biomedcentral.com)
The more recent duplication event in particular would be expected to result in many paralogous pairs of genes differing by relatively few sequence differences, thus complicating gene identification using ESTs. (biomedcentral.com)
These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
Biotin labeled cRNA transcripts were synthesized, fragmented and hybridized to HuGeneFL GeneChip probe arrays representing more than 6800 human genes and expressed sequence tags. (cdc.gov)
Identification of immune-relevant genes by expressed sequence tag analysis of head kidney from grass carp (Ctenopharyngodon idella). (openwetware.org)
Some laboratories have utilized transcriptomics to explore the response of chickpea to abiotic and biotic stresses such as drought, salinity, heat, cold, Fusarium oxysporum and Ascochyta rabiei diﬀerentially expressed genes and also established crosstalk between biotic and abiotic stress responses. (intechopen.com)
DAVID was used to perform the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis for the different expression genes (DEGs). (medscimonit.com)
Ten DEGs, including 7 hub genes from PPI analysis, were confirmed by real-time PCR. (medscimonit.com)
Analysis of 20,257 high-quality ESTs yielded 6372 unique genes comprised of 3059 tentative consensus (TC) sequences and 3313 singletons (available at http://aksoylab.yale.edu ). (umd.edu)
Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. (unboundmedicine.com)

EST approaches have largely been superseded by whole genome and transcriptome sequencing and metagenome sequencing. (wikipedia.org)
Sequencing of the A. oryzae genome was accomplished using the whole-genome shotgun (WGS) approach. (nature.com)
Phylogenetic analysis of the three aspergilli using the whole-genome data showed that A. nidulans branched off earlier than A. oryzae and A. fumigatus 5 . (nature.com)
When available, the information provided by whole-genome sequencing projects provides an entry into an understanding of genome structure and evolution and gene discovery, and function. (biomedcentral.com)
The advent of low cost and high accuracy exome and whole genome sequencing has led many global healthcare organizations to adopt genome sequencing early in managing patient populations. (cdc.gov)
High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and Whole-Genome Maps. (cdc.gov)
Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. (cdc.gov)

ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. (wikipedia.org)
Because of the way ESTs are sequenced, many distinct expressed sequence tags are often partial sequences that correspond to the same mRNA of an organism. (wikipedia.org)
When the complete genome sequence of an organism is available and transcripts are annotated, it is possible to bypass contig assembly and directly match transcripts with ESTs. (wikipedia.org)
High-throughput analyses of ESTs often encounter similar data management challenges. (wikipedia.org)
In most microarray experiments, a significant fraction of the differentially expressed mRNAs identified correspond to expressed sequence tags (ESTs) and are generally discarded from further analyses. (elsevierpure.com)
We used careful bioinformatics analyses to characterize those ESTs that were found to be highly overexpressed in a series of pancreatic adenocarcinomas. (elsevierpure.com)
The GeneExpress® software system Fold Change Analysis Tool was used and 60 ESTs were identified that were expressed at levels at least 3-fold greater in the pancreatic cancers as compared to normal tissues. (elsevierpure.com)
The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs). (nih.gov)
A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. (nih.gov)
A total of 5,542 ESTs were generated representing 4,688 unique sequences. (nih.gov)
Some of the ESTs in this collection have low sequence similarity with those in Genbank suggesting that they may encode functions that may contribute to Thellungiella's high degree of stress tolerance when compared with Arabidopsis. (mcmaster.ca)
A total of 600,000 sequencing attempts were made, generating a total of 438,321 quality ESTs. (auburn.edu)
In order to select reliable SNPs, contigs containing four or more ESTs should be used and the minor allele sequence should be represented at least twice. (auburn.edu)
Application of such quality assessment measures, along with large resources of ESTs, should provide effective means for SNP identification in species where genome sequence resources are lacking. (auburn.edu)
The parallel analysis of ESTs from the two closely related ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. (auburn.edu)
Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)

Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
For his vision in using expressed sequence tags in genetic analyses, his unique contributions to the sequencing of microbial genomes, and his leadership in mobilizing new methods and resources for sequencing the human genome. (nasonline.org)

These genome resources provide the material basis for future microarray development, marker validation, and genetic linkage and QTL analysis. (nih.gov)
Fluorescent in situ hybridisation (FISH) on metaphase chromosomes and on extended chromatin will be used to physically locate repetitive as well as single copy DNA sequences on conifer chromosomes and to integrate physical and genetic maps. (le.ac.uk)
Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. (biomedcentral.com)
Through a laborious genetic sequencing analysis, Dunn and an international team of scientists have settled the long-standing debate and determined that acoelomorpha belongs as a sister clade to other bilateral animals. (brown.edu)
The researchers reported their genetic analysis shows diminishing evidence for placing xenoturbella within Deuterostomia, one of the major groups within the animal kingdom. (brown.edu)
The researchers base their findings on an analysis that reached further into the genetic makeup of cycliophora than previous studies had done. (brown.edu)
The team used a genetic sequencing technique called expressed sequence tags to carry out the phylogenetic studies. (brown.edu)
This deep EST-SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation. (unboundmedicine.com)

In 1982, the idea of selecting random or semi-random clones from such a cDNA library for sequencing was explored by Greg Sutcliffe and coworkers. (wikipedia.org)
sequenced 178 clones from a rabbit muscle cDNA library. (wikipedia.org)
A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. (nih.gov)
Single pass sequencing of cDNA clones provides a rapid route to gene discovery and production of EST's (2). (le.ac.uk)
Systematic sequencing of cDNA clones derived from xylem and leaf tissue will produce a new generation of research tools for conifer biology. (le.ac.uk)

This makes it difficult to write programs that can unambiguously determine that two EST libraries were sequenced from the same tissue. (wikipedia.org)
In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. (biomedcentral.com)

In 1991, Adams and co-workers coined the term EST and initiated more systematic sequencing as a project (starting with 600 brain cDNAs). (wikipedia.org)

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. (mpg.de)
Syntenic analysis of the three aspergilli revealed the presence of syntenic blocks and A. oryzae -specific blocks of sequence (lacking synteny with the two other aspergilli) in a mosaic manner throughout the A. oryzae genome ( Fig. 1 ). (nature.com)

In an effort to reduce the number of expressed sequence tags for downstream gene discovery analyses, several groups assembled expressed sequence tags into EST contigs. (wikipedia.org)
Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. (nih.gov)

Segregating populations will be characterised with both single locus (microsatellites) and multi-locus (AFLPs) marker systems providing framework maps for the eventual location of cDNAs generated from single pass sequencing. (le.ac.uk)

Using this approach, we have generated a large amount of data forexpressed sequence tags, which provides an opportunity for the discovery of putative novel transcripts andalternative splice variants that could be developmentally specific to the first larval stage. (sfu.ca)
Expressedsequence tags, which map across intron-exon boundaries (around 300), indicate possible alternative splice sites,while expressed sequence tags, which map near the ends of known transcripts (around 600), suggest extensionof the coding or untranslated regions. (sfu.ca)
Suchapplication of this new sequencing technique allows for high-throughput, genome-wide experimental verificationof known and novel transcripts. (sfu.ca)
Based on the nucleotide sequence information of transcripts, we identified 819 novel transcriptionally active regions (nTARs) and revised 906 incorrectly predicted gene models, including revisions of exon-intron structure, gene orientation and sequencing errors. (biomedcentral.com)
Gene expression analyses using NGS platforms were carried out in the vegetative and reproductive tissues such as shoot, root, mature leaf, ﬂower bud, young pod, seed and nodule by various groups which resulted in identification of several tissue-specific transcripts. (intechopen.com)

A total of 101 and 119 simple sequence repeats (SSR) were obtained from expressed sequence tags (EST) of the red sea bream (Chrysophrys major) and gilthead sea bream (Sparus aurata), respectively. (hawaii.edu)
Transcriptome analysis has facilitated the development of molecular markers such as simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs) and potential intron polymorphisms (PIPs) that are being used to expedite the chickpea breeding programmes. (intechopen.com)

To analyze the regulatory mechanism involved in the high growth potential of C. virgata , we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. (frontiersin.org)
Transcriptome analysis of human gastric cancer. (genscript.com)
However, chickpea transcriptome analysis witnessed significant progress with the advent of the NGS platforms. (intechopen.com)
Transcriptome analysis has been utilized extensively to identify non-coding RNAs such as miRNAs and long intergenic non-coding (LINC) RNAs. (intechopen.com)

Over 300,000 putative SNPs have been identified, of which over 48,000 are high quality SNPs as defined by contig size of at least four sequences and the minor allele presence of at least twice in the contig. (auburn.edu)

Complete Genome Sequence of Vibrio sp. (cdc.gov)

Expressed Sequence Tag (EST) sequencing is one of the most efficient means for gene discovery and gene expression profiling. (auburn.edu)

These sequences represent the protein coding region of the PFDN6 cDNA ORF which is encoded by the open reading frame (ORF) sequence. (genscript.com)
Extensive analyses of transcriptome have been carried out in chickpea, which is the third most important legume valued as a source of dietary protein and micronutrients. (intechopen.com)
Expression analysis of the three yolk proteins indicates that all are detected in females, while only the yolk protein with similarity to lipases, is expressed in males. (umd.edu)

However, large-scale expressed sequence tag (EST) resources have been lacking for this species. (nih.gov)
An examination of the content and distribution of repetitive DNA sequences to identify the location of such sequences within specific chromosomes and their conservation across species of the Pinaceae family. (le.ac.uk)
In this study, we mined expressed sequence tag (EST) databases developed from barley and developed markers for further mapping of this region in a population derived from barley cultivars Rika and Kombar as well as did a comparative analysis of this region to other grass species. (usda.gov)
Additionally, we did a comparative analysis of this region to other grass species. (usda.gov)
Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. (unboundmedicine.com)

Comparative analysis revealed that the region containing the two resistance loci has good colinearity with rice and Brachypodium. (usda.gov)
Comparative analysis revealed that a 12.6 cM region containing the two resistance loci is colinear with a region of rice chromosome 2 between 23.7 and 29.9 Mb with only a few rearrangements, and nearly the same level of colinearity was observed between barley and Brachypodium in this region. (usda.gov)
Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (biomedcentral.com)

Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. (karger.com)

Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. (unboundmedicine.com)
Biased phylodynamic inferences from analysing clusters of viral sequences. (cdc.gov)

4 We screened the coding sequence of ESPN (GenBank accession number AL136880) by sequencing PCR amplified ESPN exons from genomic DNA of affected individuals in the two families. (bmj.com)

This work alsodemonstrates the successful and efficient application of a next generation sequencing methodology.Results: We have generated over 30 million bases of novel expressed sequence tags from first larval stage wormsutilizing high-throughput sequencing technology. (sfu.ca)
Bertelsen A.H., Velculescu V.E., High-throughput gene expression analysis using SAGE, Drug Discovery Today 3 (1998) 152-159. (gse-journal.org)

This section aims to summarise and discuss existing analyses and explanations of tense variation: the switching back and forth between -ta (past tense) and -ru (non-past tense) that can be seen in Japanese narratives describing past events. (lu.se)

We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean ( Glycine max L. Merr. (biomedcentral.com)

Among the unigenes, 94.1% encoded products that were most similar in amino acid sequence to Arabidopsis and 1.5% had no match with a member of the family Brassicaceae. (mcmaster.ca)
Unigenes from the cold library were more similar to Arabidopsis sequences than either drought- or salinity-induced sequences, indicating that latter responses may be more divergent between Thellungiella and Arabidopsis. (mcmaster.ca)
Analysis of gene ontology using the best matched Arabidopsis locus showed that the Thellungiella unigenes represented all biological processes and all cellular components, with the highest number of sequences attributed to the chloroplast and mitochondria. (mcmaster.ca)

An annotated genomic sequence of the corn anthracnose fungus Colletotrichum graminicola has been published previously, but correct identification of gene models by means of automated gene annotation remains a challenge. (biomedcentral.com)
The EST resource should also be valuable for identification of microsatellites, comparative genome analysis. (auburn.edu)
This large scale EST sequencing project would allow the identification of majority of catfish transcriptome. (auburn.edu)
The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (biomedcentral.com)
2009. Identification and functional characterisation of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida . (hutton.ac.uk)

GOblet: annotation of anonymous sequence data with Gene Ontology and pathway terms. (mpg.de)

In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. (nih.gov)
The derived amino acid sequence of Ov-phy-1 encoded a peptide that was most similar to the two Caenorhabditis elegans prolyl 4-hydroxylase homologues and to the isoform II enzymes of vertebrates. (embl.de)
SLC6A19 is a sodium-dependent and chloride-independent neutral amino acid transporter, expressed predominately in the kidneys and intestine. (medscape.com)

In the Fp subunit of SQR, and the closely related membrane-associated fumarate reductase of anaerobic organisms, FAD is covalently attached via an 8α-N(3)-histidyl linkage to a histidine (His) in a conserved sequence in the N-terminal part of the polypeptide. (lu.se)

Time will tell if such collaborations can be developed and maintained, but failure to do so would seem a missed opportunity to generate clinical utility data for using genome sequencing as a screening tool to prevent disease and improve population health. (cdc.gov)

Gene expression patterns in human liver cells exposed to tetrachloroethylene and it's metabolite using microarray analysis. (cdc.gov)

To develop a foundation for tsetse physiology, a normalized expressed sequence tag (EST) library was constructed from fat body tissue of immune-stimulated Glossina morsitans morsitans. (umd.edu)

Single-gene knockout-coupled omics analysis identifies C9orf85 and CXorf38 as two uncharacterized human proteins associated with ZIP8 malfunction. (nih.gov)

Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola . (biomedcentral.com)
The differential gene expression data analysis was performed using GeneChip 4.0 software. (cdc.gov)
Discovery science in genomic medicine has generally enjoyed longstanding large collaborations for data sharing and joint analyses. (cdc.gov)
These early adopters have taken a leap of faith that having genome sequence data readily at hand to guide health management will eventually yield improved health outcomes. (cdc.gov)
The existence of early adopter organizations generating sequence data on large numbers of individuals with paired longitudinal electronic health record data provides opportunities for real-world clinical research directed at health outcome endpoints. (cdc.gov)
Barriers to pooling efforts include lack of data standards, lack of common outcome metrics, lack of infrastructure that would allow aggregation and analysis of clinical and genomic data, and lack of programs that incentivize data sharing. (cdc.gov)

Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)

They may be represented in databases as either cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand. (wikipedia.org)
This lack of increase contrasts with previous reports as does the mRNA length: this is 50% larger as confirmed by sequencing the 3' end. (embl.de)

In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. (wikipedia.org)

An EST results from one-shot sequencing of a cloned cDNA. (wikipedia.org)

In: Expressed sequence tags - generation and analysis, Methods in Molecular Biology Vol. 533 (J. Parkinson, ed. (umontreal.ca)

In November, 2017, the NASEM Roundtable on Genomics and Precision Health held the workshop, " Implementing and Evaluating Genomic Screening Programs in Health Care Systems , " which explored the emerging landscape of worldwide organizations that are (or soon will be) applying genome sequencing as a screening tool in populations. (cdc.gov)
Additionally, attendees broadly expressed the perspective that health care disparities for genomic applications in underserved populations are an existing and expanding issue no matter the level of evidence of clinical utility. (cdc.gov)

In the most computationally intensive phylogenetic analysis to date, an international research team led by Brown University has found the first evolutionary branching for bilateral animals. (brown.edu)
Dunn called the effort the most computationally intensive phylogenetic analysis to date. (brown.edu)

DNA sequence and analysis of human chromosome 9. (nih.gov)

Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (biomedcentral.com)
Soybean has a large (1115 Mbp) genome that has yet to be fully sequenced. (biomedcentral.com)
The workshop concluded with substantial momentum directed at finding concrete ways to enhance collaboration across organizations that have, or soon will have, genome sequencing programs for large population groups. (cdc.gov)

Anatomy9

Organisms15

Chemicals and Drugs13

Analytical, Diagnostic and Therapeutic Techniques and Equipment18

Phenomena and Processes42

Disciplines and Occupations3

Technology, Industry, Agriculture4

Information Science12

Health Care1

Genes27

Whole genome7

ESTs16

Genomes4

Genetic8

Clones5

Libraries2

Systematic1

Synteny2

Contigs2

CDNAs1

Transcripts5

Simple sequenc2

Transcriptome Analysis4

Putative1

Complete genome sequence1

Gene discovery1

Protein3

Species5

Loci3

Similarity1

Clusters2

Genbank1

High-throughput2

Variation1

45,0001

Arabidopsis3

Identification5

Annotation1

Amino3

Linkage1

Generate1

Microarray analysis1

Tissue1

Proteins1

Data6

Multigene1

MRNA2

Genetics1

Results1

Methods1

Populations2

Phylogenetic2

Chromosome1

Large3