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  • sequences
  • Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. (rna-seqblog.com)
  • cell
  • Additional genes related to cytokines, cell proliferation, and other processes were also identified. (biomedcentral.com)
  • One example was a strong correlation between high proliferation rates in metastatic cancers and overexpression of genes that participate in cell cycle regulation, DNA replication, and DNA repair. (aacrjournals.org)
  • variable
  • Using as their benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), they assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. (rna-seqblog.com)
  • existing cluster
  • A popular approach to class discovery involves grouping similar genes or samples together using one of the many existing clustering methods such the traditional k-means or hierarchical clustering , or the more recent MCL and clust methods. (wikipedia.org)
  • tumors
  • The laboratory test is a signature of 31 genes, 28 discriminating genes and 3 control genes, that classifies tumors as class 1 (low risk of metastasis) or class 2 (high risk of metastasis), using reverse transcription polymerase chain reaction (RT-PCR) on formalin-fixed paraffin-embedded (FFPE) primary tumor tissue specimens obtained from either biopsy or excision of a cutaneous melanoma. (unicare.com)
  • The clinical validity of the DecisionDx-Melanoma test was evaluated in a prospective, multicenter study of class 1 cutaneous melanoma tumors which analyzed microarray expression data to identify a prognostic 28-gene signature to predict risk of metastasis (Gerami, 2015b). (unicare.com)
  • The investigators suggested their preliminary analysis indicates the 28-gene signature is an independent predictor of metastasis risk in the studied cohort of cutaneous melanoma tumors. (unicare.com)
  • In the context of cancer, gene expression profiling has been used to more accurately classify tumors. (wikipedia.org)
  • Presented below are ways that gene expression profiling has been used to more precisely classify tumors into subgroups, often with clinical effect. (wikipedia.org)
  • The highest expression in developmental stage is the blastocyst and for health state, it is most found in uterine tumors. (wikipedia.org)
  • Studies on lung cancer have also shown that squamous cell carcinomas give rise to tumors with elevated K5 levels, and that they are more likely to arise from stem cells expressing K5 than from those cells without K5 expression. (wikipedia.org)
  • sequences
  • Sequence based techniques, like RNA-Seq , provide information on the sequences of genes in addition to their expression level. (wikipedia.org)
  • The genetic basis for disease is determined by the inheritance of genes containing specific sequences of deoxyribonucleic acid (DNA). (uptodate.com)
  • d) for each distinctly sized amplification product detected in step (c), calculating a cycle number, C t , where the amount of that amplification product crosses a predefined threshold, and correlating the threshold cycle with the amount of a nucleic acid having a sequence of interest in said sample, wherein said method provides an amplification profile and a relative abundance for members of said set of nucleic acid sequences of interest. (google.ca)
  • The Polymerase Chain Reaction (PCR), with its sensitive and selective amplification of specific nucleic acid sequences has become a research tool of almost unparalleled importance, with applications in, for example, cloning, gene expression analysis, DNA sequencing, genetic mapping and diagnostics. (google.ca)
  • DNA labeled with fluorophores (target) is prepared from a sample such as a tumor biopsy and is hybridized to the complementary DNA (cDNA) sequences on the gene chip. (wikipedia.org)
  • A reverse northern blot can be used to profile expression levels of particular sets of RNA sequences in a tissue or to determine presence of a particular RNA sequence in a sample. (wikipedia.org)
  • Due to a tendency to generate high numbers of false positives caused by band contamination with heterogeneous sequences, differential display hits will need to be confirmed by an alternative method for determining differential expression. (wikipedia.org)
  • Therefore, reverse northern has been used as one means of confirming hits from DD-PCR, or sequences with altered expression levels. (wikipedia.org)
  • protein
  • Protein KIAA1958 is a protein that in humans is encoded by the KIAA1958 gene. (wikipedia.org)
  • The gene has these neighbors on chromosome 9: HSDL2: Hydroxysteroid dehydrogenase-like protein 2 plays a role in nucleotide binding, oxidoreductase activity, and sterol binding. (wikipedia.org)
  • Keratin 5, also known as KRT5, K5, or CK5, is a protein that is encoded in humans by the KRT5 gene. (wikipedia.org)
  • The c10orf35 protein has expression over the 75th percentile in the brain, spinal chord, and male reproductive organs. (wikipedia.org)
  • These included Ribulose-1,5-bisphosphate carboxylase oxygenase activase, which regulates the photosynthetic enzyme RuBisCO, GAPDH, which is involved in glycolysis and oxidative stress response, as well as cell division control protein CDC91 and the NBS-LLR disease resistance gene. (wikipedia.org)
  • In this technique, DNA coding for a protein of interest is cloned using polymerase chain reaction (PCR), and/or restriction enzymes into a plasmid ( expression vector). (wikipedia.org)
  • Chromosome 20 open reading frame 111, or C20orf111, is the hypothetical protein that in humans is encoded by the C20orf111 gene. (wikipedia.org)
  • C20orf111 a valid, protein coding gene that is found on the minus strand of chromosome 20 at q13.12 by searching the UCSC Genome Browser, but q13.11 according to Refseq on NCBI. (wikipedia.org)
  • Krueppel-like factor 6 is a protein that in humans is encoded by the KLF6 gene. (wikipedia.org)
  • The DNA binding and transcriptional activity of this protein, in conjunction with its expression pattern, suggests that this protein may participate in the regulation and/or maintenance of the basal expression of pregnancy-specific glycoprotein genes and possibly other TATA box-less genes. (wikipedia.org)
  • Chromatin assembly factor 1 subunit A is a protein that in humans is encoded by the CHAF1A gene. (wikipedia.org)
  • cellular
  • Though cytotoxic-crossmatch assay can predict rejection mediated by cellular immunity, genetic-expression tests specific to the organ type to be transplanted, for instance AlloMap Molecular Expression Testing, have a high negative predictive value. (wikipedia.org)
  • variants
  • Otherwise, the number of mismatched gene variants, namely alleles, encoding cell surface molecules called major histocompatibility complex (MHC), classes I and II, correlate with the rapidity and severity of transplant rejection. (wikipedia.org)
  • humans
  • The FAM98A gene is located on 2p22.3 in humans on the "-" (minus) strand. (wikipedia.org)
  • Because there are three paralogs of FAM98 in humans, there is a common ancestor of these genes. (wikipedia.org)
  • When looking at the EST Profiles in humans, normal tissue (non-cancerous), expresses at a level of 82 transcripts per million. (wikipedia.org)
  • tumor
  • The DecisionDx-Melanoma test (Castle Bioscience, Inc., Friendswood, TX) is a multigene expression assay designed to predict metastasis in individuals with stage I or stage II cutaneous melanoma who have no sign of disease beyond the original tumor. (unicare.com)
  • Because of these selective properties, the majority of cells within a tumor will share a common profile of gene expression. (wikipedia.org)
  • Of note, similar gene expression patterns associated with metastatic behaviour of breast cancer tumor cells have also been found in breast cancer of dog, the most common tumor of the female dog. (wikipedia.org)
  • It is a tumor suppressor gene. (wikipedia.org)
  • analyses
  • Analyses of gene expression can be clinically useful for disease classification, diagnosis, prognosis, and tailoring treatment to underlying genetic determinants of pharmacologic response. (uptodate.com)
  • assay
  • Berger and colleagues (2016) performed a retrospective chart review of 156 individuals with cutaneous melanoma who were consecutively tested with the DecisionDx-Melanoma gene expression profile assay at three dermatology and three surgical oncology practices between May 2013 and December 2015. (unicare.com)
  • measurement
  • Illumina RNA-Seq solutions provide precise measurement of strand orientation, uniform coverage, and high confidence mapping of alternate transcripts and gene fusions. (illumina.com)
  • provides
  • RNA-Seq provides a unique combination of transcriptome-wide coverage, sensitivity, and accuracy for a comprehensive view of gene expression changes. (illumina.com)
  • Although DNA Microarrays and newer next-generation techniques have generally supplanted reverse northern blotting, it is still utilized today and provides a relatively cheap and easy means of defining expression of large sets of genes. (wikipedia.org)
  • classification
  • A full classification includes histopathological type, grade, stage (TNM), receptor status, and the presence or absence of genes as determined by DNA testing: Histopathology. (wikipedia.org)
  • genome
  • Most of the genome is selectively repressed, a property that is governed by the regulation of gene expression, mostly at the level of transcription (ie, the production of messenger RNA from the DNA). (uptodate.com)
  • cell
  • the sequence tells us what the cell could possibly do, while the expression profile tells us what it is actually doing at a point in time. (wikipedia.org)
  • Many factors determine whether a gene is on or off, such as the time of day, whether or not the cell is actively dividing, its local environment, and chemical signals from other cells. (wikipedia.org)
  • Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. (springer.com)
  • Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors. (springer.com)
  • Approximately 3 to 5 percent of genes are active in a particular cell, even though all cells have the same information contained in their DNA. (uptodate.com)
  • The unique pattern of gene expression for a given cell or tissue is referred to as its molecular signature. (wikipedia.org)
  • involves
  • A popular approach to class discovery involves grouping similar genes or samples together using k-means or hierarchical clustering. (wikipedia.org)
  • actively
  • These profiles can, for example, distinguish between cells that are actively dividing, or show how the cells react to a particular treatment. (wikipedia.org)
  • Gene expression analysis studies can provide a snapshot of actively expressed genes and transcripts under various conditions. (illumina.com)
  • applications
  • This chapter will first review the various techniques used in gene expression profiling (GEP), and then present the pertinent practical applications of the data acquired by GEP in diagnostic hematopathology, as summarized in various tables, referenced throughout the text. (springer.com)
  • analysis
  • Cluster analysis has placed a group of down regulated genes in the upper left corner. (wikipedia.org)
  • Terry Speed (ed.) (2003) Statistical Analysis of Gene Expression Micro-array Data . (springer.com)
  • The advent of next-generation sequencing has made sequence based expression analysis an increasingly popular, "digital" alternative to microarrays called RNA-Seq. (primidi.com)
  • Our tools provide efficient mechanical disruption of difficult-to-lyse microbes, optimized chemistry for high yields of nucleic acids, and accurate qPCR-based gene expression analysis to facilitate and advance your research. (qiagen.com)
  • Illumina offers comprehensive next-generation sequencing (NGS) solutions that provide high-quality gene expression and transcriptome analysis data for a broad range of sample types. (illumina.com)
  • known
  • Most early expression profiling experiments, and many current ones, have this form which is known as class discovery. (wikipedia.org)
  • Current cancer research makes use primarily of DNA microarrays in which an arrayed series of microscopic spots of pre-defined DNA oligonucleotides known as probes are covalently attached to a solid surface such as glass, forming what is known as a gene chip. (wikipedia.org)
  • A few of the known genes near C20orf111 are given in the box below with their known function. (wikipedia.org)
  • sequences
  • Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. (rna-seqblog.com)
  • cell
  • Additional genes related to cytokines, cell proliferation, and other processes were also identified. (biomedcentral.com)
  • One example was a strong correlation between high proliferation rates in metastatic cancers and overexpression of genes that participate in cell cycle regulation, DNA replication, and DNA repair. (aacrjournals.org)
  • variable
  • Using as their benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), they assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. (rna-seqblog.com)
  • proteins
  • With the GeoVax vaccine a variety of HIV proteins (both surface and internal) are expressed from genes which include the Env, Pol and Gag genes. (wikipedia.org)
  • These proteins in turn activate other genes, resulting in a cascading network of activity. (wikipedia.org)
  • In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some, if not most, of them are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution. (wikipedia.org)
  • ligand
  • Biomarkers such as programmed death receptor 1 ligand (PD-L1) expression, tumor mutational burden (TMB), and high microsatellite instability are potentially applicable to predict the efficacy of immune checkpoint blockade (ICB). (aacrjournals.org)
  • regulate
  • Kinmonth-Schultz HA, Tong X, Lee J, Song YH, Ito S, Kim S-H, Imaizumi T (2016) Cool night-time temperatures induce the expression of CONSTANS and FLOWERING LOCUS T to regulate flowering in Arabidopsis. (washington.edu)
  • FUNCTION
  • FUNCTION: [Summary is not available for the mouse gene. (utsouthwestern.edu)
  • He was awarded a PhD from the University of Edinburgh in 1989 for research investigating the structure and function of the malate synthase gene in cucumber supervised by Steven M. Smith and Chris J. Leaver. (wikipedia.org)
  • Structure and function of the cucumber malate synthase gene and expression during plant development. (wikipedia.org)
  • interest
  • He has a long-standing interest in identifying genes, which when altered can cause leukemia and other cancers. (wikipedia.org)
  • reference
  • To streamline reference gene selection, we offer PCR primers for a set of commonly used reference genes that can be used individually, easily screened using our preplated 96-well and 384-well reference panels or added to custom-designed plates. (bio-rad.com)
  • available
  • One or more of the preceding sentences incorporates text from the royalsociety.org website where: "All text published under the heading 'Biography' on Fellow profile pages is available under Creative Commons Attribution 4.0 International License. (wikipedia.org)
  • foreign
  • The vaccine works with a combined DNA vaccine and MVA (modified vaccinia Ankara) vaccine both of which lead to the insertion of genes into primate DNA which leads to foreign protein expression. (wikipedia.org)
  • results
  • Preliminary results indicate an excellent safety profile and highly reproducible immunogenicity subsequently confirmed by the official publication above in The Journal of Infectious Diseases. (wikipedia.org)
  • discovery
  • The discovery of a novel Cytochrome P450 - oxidoreductase gene fusion described the last unknown step in synthesis of morphine and codeine. (wikipedia.org)