• For example, in the hereditary cancer syndromes familial adenomatous polyposis or hereditary nonpolyposis colorectal cancer, mutations have been discovered in the APC gene and DNA mismatch repair genes. (medscape.com)
  • Hereditary breast cancers linked to germ-line mutations of BRCA1 and BRCA2 genes almost invariably show allelic imbalance (Al) at the respective loci. (lu.se)
  • A condition caused by harmful mutations in two different genes. (gene.vision)
  • A group of inherited conditions caused by mutations in any one of more than 300 genes that eventually leads to gradual degeneration of photoreceptor cells in the retina and subsequent visual loss. (gene.vision)
  • These genes are more likely to acquire harmful mutations, the authors say, and therefore, could act as biomarkers for predicting or diagnosing disease. (the-scientist.com)
  • Biallelic genes, on the other hand, are much more evolutionarily conserved and are more likely to be associated with cell survival, Gregg explains, meaning they're less likely to tolerate mutations. (the-scientist.com)
  • Activating mutations of Ras genes are often observed in cancer. (nature.com)
  • As we also saw in that blog post, mutations that change gene expression are often associated with harmful effects. (knime.com)
  • Rapid evolution of the mitochondrial genome, including fixation of both adaptive and deleterious mutations, creates intrinsic selection pressures favoring nuclear gene mutations that maintain mitochondrial function. (escholarship.org)
  • We characterized point mutations, insertions, deletions and chromosomal allelic imbalance. (tmc.edu)
  • During these processes, the cancer cells acquire multiple allelic mutations in genes such as proto-oncogenes, tumour suppressor (TS) genes and other genes that control cell proliferation ( Hahn and Weinberg, 2002 ). (kdwis.com)
  • Recent technological advancements in the characterization of ctDNA, 5 7-9 including those to inform therapy selection through detection of EGFR gene mutations or other actionable changes in panels of genes 10-12 have demonstrated the feasibility and clinical utility of blood-based tests to guide the clinical management of patients with cancer, typically at late stages. (bmj.com)
  • In conclusion, the high prevalence of Al at BRCA1 in BRCA2 mutation tumours and vice versa suggests that somatic events occurring at the other breast cancer susceptibility gene locus may be selected in the cancer development. (lu.se)
  • and somatic copy-number aberration (SCNA), fragment length, fragment endpoint, and allelic imbalance data from WG sequencing (WGS). (esmo.org)
  • In female eutherian mammals, dosage compensation of X-linked genes between the two sexes (XX & XY) is achieved by random XCI in adult somatic tissues. (xuwang.us)
  • alleleIntegrator searches for allelic imbalances that represent cancer-defining somatic copy number changes to precisely identify single cancer cell transcriptomes. (sanger.ac.uk)
  • Breast Cancer Research, 2011 "Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer", for which we have made a pre-release with 2.0 functionality available: [#pre-release BAFsegmentation 2.0pre]. (lu.se)
  • The Mcs7 quantitative trait locus is associated with an increased susceptibility to mammary cancer in congenic rats and an allele-specific imbalance. (mcw.edu)
  • Together, these data suggest that one or more breast cancer-related genes are located within the dominantly acting WKy allele at the Mcs7 locus. (mcw.edu)
  • The minimum region of human chromosome 11 that contained the KAI1 gene was located on the proximal region of 11p11.2 divided by the D11S554 locus. (johnshopkins.edu)
  • ZNF331 is imprinted in human term placenta and might be a new ubiquitously imprinted gene, part of a primate-specific locus. (ox.ac.uk)
  • Demonstration of partial imprinting of PHACTR2 calls for re-evaluation of the allelic pattern of expression for the PHACTR2-PLAGL1 locus. (ox.ac.uk)
  • Allelic imbalance analysis in the METH-2 locus Allelic imbalance (AI) in METH-2 was assessed in 23 normal/tumour pairs using an intragenic, intronic solitary nucleotide polymorphism (SNP): rs1552330 (NCBI). (healthyguide.info)
  • We show that differential allelic expression is common among these 12 candidate genes and is comparable between breast and blood (fresh and transformed lymphoblasts) in a significant proportion of them. (springer.com)
  • Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. (snpedia.com)
  • An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3. (snpedia.com)
  • RESULTS: Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. (ox.ac.uk)
  • The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. (ox.ac.uk)
  • We performed exome sequencing of samples from 12 FAP patients to characterize adenomas and to identify candidate genes of adenoma development that may serve as potential targets for chemoprevention drug development. (tmc.edu)
  • Excluding the known genes APC and KRAS, 50 candidate genes were identified that are putatively involved in the early development of CRC. (tmc.edu)
  • Do candidate genes increase clinical utility of hereditary cancer panels? (ambrygen.com)
  • 2 Several such genetic alterations have been characterized in candidate genes encoding molecules important for pain transmission, which result in impaired function of these gene products to ultimately impact the efficacy and side effect profiles of several analgesics, thus defining the active field of pharmacogenomics in pain medicine. (ahdbonline.com)
  • Learn more about DNA, genes and chromosomes . (gene.vision)
  • There are some more common exceptions, however, such as how cells with two X chromosomes inactivate one of them during development in order to meter the expression level of X-linked genes that can be toxic in double doses. (the-scientist.com)
  • In oral SCC, modern DNA technology, especially allelic imbalance (loss of heterozygosity) studies, have identified chromosomal changes suggestive of the involvement of tumor suppressor genes (TSGs), particularly in chromosomes 3, 9, 11, and 17. (medscape.com)
  • Genes, chromosomes & cancer 2017 11 57 (3): 140-149. (cdc.gov)
  • Polymorphic variants at regulatory elements can cause differential allelic expression (DAE), thus using DAE as a quantitative trait could help identify such variation. (springer.com)
  • PMID 17173513 ] No association between variants in the ACE and angiotensin II receptor 1 genes and acute mountain sickness in Nepalese pilgrims to the Janai Purnima Festival at 4380 m. (snpedia.com)
  • PMID 21709586 ] Common variants of the ACE gene and aneurysmal subarachnoid hemorrhage in a Danish population: a case-control study. (snpedia.com)
  • Alternatively spliced transcript variants have been identified for this gene. (cancerindex.org)
  • We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. (bvsalud.org)
  • In addition, we show that AD variants exhibit allelic imbalance on target gene expression. (bvsalud.org)
  • MyChoice CDx is the first and only FDA-approved tumor test that determines homologous recombination deficiency status by detecting BRCA1 and BRCA2 (sequencing and large rearrangement) variants and assessing genomic instability using three critical biomarkers: loss of heterozygosity, telomeric allelic imbalance and large-scale state transitions. (myriadgenetics.eu)
  • Germline predisposition to pediatric Ewing sarcoma is characterized by inherited pathogenic variants in DNA damage repair genes. (cdc.gov)
  • Variants in blood pressure genes and the risk of Accardi R, Rubino R, Scalise M et col . (2011). (who.int)
  • A total of 7 possible genetic alterations and epigenetic changes in CAFs are discussed, including gene differential expression, karyotype analysis, gene copy number variation, loss of heterozygosis, allelic imbalance, microsatellite instability, post‑transcriptional control and DNA methylation. (spandidos-publications.com)
  • Differential allelic expression (DAE) in heterozygote individuals could be used to develop a new approach to discover regulatory breast cancer susceptibility loci. (springer.com)
  • Differential allelic expression ratios were determined by Taqman assay. (springer.com)
  • Our findings support the use of differential allelic expression in blood as a surrogate for breast tissue in future studies on predisposition to breast cancer. (springer.com)
  • We aimed to perform a more extensive evaluation of differential allelic expression between blood and breast in order to assess the potential usefulness of LCL and fresh blood in association studies, to identify regulatory polymorphisms related to susceptibility to breast cancer. (springer.com)
  • SEESAW allows for testing global allelic imbalance across all samples (pairwise testing within each individual), as well as differential, or dynamic allelic imbalance (pairwise allelic fold changes estimated within individual, followed by testing across two groups, or along an additional covariate). (riken.jp)
  • In three examples, we perform global AI testing, differential AI testing, and dynamic AI testing, in all cases on simulated data associated with human genes. (riken.jp)
  • More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. (ox.ac.uk)
  • Corrigendum: analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. (tamu.edu)
  • As a control, they tested whether the method could distinguish X-linked genes from autosomal genes, and indeed, the model labeled X-linked genes as RAE, validating the model's ability to discern biased expression of alleles. (the-scientist.com)
  • Burst-Like Transcription of Mutant and Wildtype MYH7-Alleles as Possible Origin of Cell-to-Cell Contractile Imbalance in Hypertrophic Cardiomyopathy. (crossref.org)
  • Breast cancer susceptibility genes BRCA1 and BRCA2 are tumour suppressor genes the alleles of which have to be inactivated before tumour development occurs. (lu.se)
  • A phenomenon where the two alleles of a given gene are expressed at different levels, either due to epigenetic inactivation of one of the two alleles, or because of genetic variation in the regulatory regions. (gene.vision)
  • Even though these copies tend to be functionally redundant, conventional genetic theory dictates that biallelic expression, wherein both alleles are transcribed equally when the gene is expressed, is nearly universal. (the-scientist.com)
  • Using a model that characterizes patterns in allele expression from bulk RNA sequencing data, the researchers found that both alleles of some genes were equally active throughout tissues-but for almost 3,000 genes, cells favored one allele or the other, exhibiting what the authors call random allelic expression (RAE). (the-scientist.com)
  • We] discovered that there are some genes where the two alleles are absolutely in lockstep with each other," Gregg explains. (the-scientist.com)
  • The researchers then compared the relative gene expression levels of each allele across different tissues within each individual, theorizing that if two alleles are expressed in a biallelic fashion, the overall allelic expression ratio should fit a binomial distribution, whereas randomly expressed alleles wouldn't. (the-scientist.com)
  • Half of the tumours (4/8) showed a physical deletion of the BRCA1 gene by FISH. (lu.se)
  • Combined allelic loss of both BRCA1 and BRCA2 gene was seen in 12 of the 17 (71%) informative hereditary tumours, whereas copy number losses of both BRCA genes was seen in only 4/14 (29%) sporadic control tumours studied by FISH. (lu.se)
  • Identification of high-penetrance breast cancer genes such as Brca1 has been accomplished by analysing familial cases. (mcw.edu)
  • Of the 31 genes, the 21 upregulated genes were primarily associated with cell paracrine and intracellular signaling, transcription regulation and cell adhesion and migration, and their transcriptional products included transforming growth factor-β2 (TGF-β2), insulin-like growth factor-binding protein 2 and transcriptional factor AP-2α/γ ( 11 ). (spandidos-publications.com)
  • Background Technological advances involving RNA-Seq and Bioinformatics allow quantifying the transcriptional levels of genes in cells, tissues, and cell lines, permitting the identification of Differentially Expressed Genes (DEGs). (researchgate.net)
  • Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. (researchgate.net)
  • Differentially expressed genes are discovered using R and then displayed in an interactive view. (knime.com)
  • This data then gets used in the R Snippet to find differentially expressed genes. (knime.com)
  • Six genes were found differentially expressed but none imprinted. (ox.ac.uk)
  • Genomic defects in DNA mismatch repair (MMR) genes (MSH2, MLH1, PSM2 or MSH6) and consequent high-frequency microsatellite instability (MSI) characterize the HNPCC syndrome [ 1 , 2 ]. (oncotarget.com)
  • Wanting to extend the findings to human tissue, he enlisted his former postdoc Stephanie Kravitz to analyze a bulk RNAseq dataset from the genotype tissue expression (GTEx) consortium that included sequences from more than 15,000 genes in 54 tissues from 832 human donors. (the-scientist.com)
  • utilizes a combination of high-resolution comparative genomic hybridization, short hairpin RNA inhibition of target genes at the locations of focal genomic deletions, and a primed cell mosaic mouse model to identify novel tumor suppressors in hepatocellular carcinoma. (biomedcentral.com)
  • Neuroblastoma is a major childhood cancer arising from precursor cells of the sympathetic nervous system which is known to acquire deletions and alterations in the expression patterns of PTPRD , indicating a potential tumor suppressor function for this gene. (biomedcentral.com)
  • Normal gene expression variation is thought to play a central role in inter-individual variation and susceptibility to disease. (springer.com)
  • Impact of microRNA-375 and its target gene SMAD-7 polymorphism on susceptibility of colorectal cancer. (cdc.gov)
  • [ 1 ] Identifying candidate precursors or enabling genes may pave the way for cancer screening, as with the ret proto-oncogene and medullary thyroid carcinoma . (medscape.com)
  • A few gene therapy trials now target head and neck cancer, which makes up only 4% of all cancers but has a dismal prognosis in advanced stages. (medscape.com)
  • p21 and other tumor suppressor genes' inactivation are therefore most likely involved in the first steps of the cancer model, with later stages possibly involving protooncogene activation and inflammation. (medscape.com)
  • DNA damage affects the expression of a variety of genes, including proto-oncogenes and cancer suppressor genes. (frontiersin.org)
  • Changes in the activity of proto-oncogenes and cancer suppressor genes are crucial in tumorigenesis ( 4 ). (frontiersin.org)
  • Background There is an availability of omics and often multi-omics cancer datasets on public databases such as Gene Expression Omnibus (GEO), International Cancer Genome Consortium and The Cancer Genome Atlas Program. (researchgate.net)
  • Ras genes are mutated in ~20% of all human cancer cases [ 1 ]. (nature.com)
  • We recently isolated the KAI1 gene, a metastasis suppressor gene for prostate cancer, from human chromosome region 11p13-cen-containing rat prostate cancer cells. (johnshopkins.edu)
  • The present study was performed to further locate the region of the KAI1 gene on the short arm of chromosome 11, and to examine whether loss of this region is significant during progression of human prostate cancer. (johnshopkins.edu)
  • These findings demonstrate a high frequency of LOH or allelic imbalance at the centromeric region of 11p, which contains the KAI1 gene in advanced prostate cancer. (johnshopkins.edu)
  • Polymorphism of SMAD7 gene (rs2337104) and risk of colorectal cancer in an Iranian population: a case-control study. (cdc.gov)
  • Intronic polymorphisms of the SMAD7 gene in association with colorectal cancer. (cdc.gov)
  • MicroRNA-binding site polymorphisms in genes involved in colorectal cancer etiopathogenesis and their impact on disease prognosis. (cdc.gov)
  • We identified colon and duodenum gene expression signatures of FAP patients and screened them against drug-induced signatures using our Cancer in-silico Drug Discovery (CiDD) software. (tmc.edu)
  • The 'cancer platform' concept proposes that most oncogenic molecules also have the inherent ability to activate tumor suppressor genes or pathways through oncogene-induced apoptosis or senescence, thus limiting their oncogenic effects in a homeostatic fashion. (biomedcentral.com)
  • Gene alterations were ranked according to OncoKB therapeutic levels of evidence (LE) from the Memorial Sloan Kettering Cancer Center. (esmo.org)
  • alleleIntegrator enables researchers to identify cancer cells in single-cell experiments that explore gene activity and function. (sanger.ac.uk)
  • These imbalances are the result of cancer-defining changes in DNA that take place over a person's lifetime. (sanger.ac.uk)
  • BAFsegmentation = BAFsegmentation is a method to identify regions of allelic imbalance from B allele frequencies obtained from SNP arrays described in ''Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays''[[BR]]J. Staaf, D. Lindgren, J. Vallon-Christersson, A. Isaksson, H. Göransson, G. Juliusson, R. Rosenquist, M. Höglund, Å. (lu.se)
  • The present review summarizes the recent achievements in understanding the gene profiles of CAFs and pays special attention to their possible epigenetic alterations. (spandidos-publications.com)
  • in 67% of the adenocarcinomas and 50% of squamous cell carcinomas, indicating that epigenetic mechanisms are involved in silencing this gene in NSCLC. (healthyguide.info)
  • One research interest is genetic and epigenetic regulation of gene expression in vertebrates and insects. (xuwang.us)
  • Using comparative, evolutionary and functional genomic approaches, we profiled genome-wide allelic imbalance in mammalian placental samples including marsupials, mouse, cattle, dog and interspecific equid hybrids (mules and hinnies), and characterized different forms of X chromosome inactivation and their epigenetic regulation in the placenta. (xuwang.us)
  • In this paper, we propose a novel module detection algorithm based on topology potential and spectral clustering algorithm to detect co-expressed modules in gene co-expression networks. (biomedcentral.com)
  • To get biologically relevant information, it is necessary to perform module (or community) detection in gene co-expression networks. (biomedcentral.com)
  • CONCLUSIONS: Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. (ox.ac.uk)
  • in one study, 31 genes in breast CAFs, which were identified using Affymetrix Human Genome U133 Plus 2.0 and an empirical Bayesian model, were different from those in NFs ( 11 ). (spandidos-publications.com)
  • Advances in massively parallel sequencing enable the rapid sequencing of this RNA (RNA-Seq) in a genome-wide manner in order to quantify the amount of synthesized gene product. (knime.com)
  • Subsequently, these reads are mapped back to the reference genome to identify the genes from which they originated. (knime.com)
  • Some RNA-seq reads will map to non-transcript/gene defined regions on the genome. (usegalaxy.org)
  • Another research interest is the DNA methylation evolution, sex-biased gene expression, host-microbe interaction, mitochondrial-nuclear genome interaction, telomeric repeat and satellite repeat evolution using the model of parasitoid jewel wasps . (xuwang.us)
  • New features include: * Improved plotting, including a new across assays plot of regions of allelic imbalance for each chromosome and whole genome plots for each assay. (lu.se)
  • 53% of these tumours showed a copy number loss of the BRCA2 gene by FISH. (lu.se)
  • RAS gene polymorphisms, classical risk factors and the advent of coronary artery disease in the Portuguese population. (snpedia.com)
  • Furthermore, very few polymorphisms were identified among the resistant individuals suggesting allelic imbalance. (usda.gov)
  • Many alignments in your dataset aren't to genes, but rather intronic or intergenic regions. (usegalaxy.org)
  • Allelic imbalance in METH-2 was assessed by an intronic solitary nucleotide polymorphism (SNP) assay and observed in 44% of helpful primary samples. (healthyguide.info)
  • Genetic alterations include genetic mutation, gene copy number variation (CNV), loss of heterozygosity (LOH), allelic imbalance (AI) and microsatellite instability (MSI). (spandidos-publications.com)
  • Naturally occurring genetic variations (present in at least 1% of the population) in a single nucleotide, DNA sequence, gene or chromosome that have no adverse effects on the individual. (gene.vision)
  • However, these genes occur at low frequency and do not account for the majority of genetic risk. (mcw.edu)
  • Several scenarios now appear to satisfactorily explain this phenomenon, including cases where differences in mtDNA genetic load may drive introgression or where co-introgression of coadapted nuclear genes may support the function of introgressed mtDNA. (escholarship.org)
  • In this context, several ontologies and data integration initiatives have emerged in recent years for the biological area, such as the broadly used Gene Ontology that contains metadata to annotate. (researchgate.net)
  • By performing a gene ontology analysis, which annotates the molecular targets and biological processes associated with a group of genes, the researchers found that RAE genes were more likely to be involved in immune adaptability and cellular plasticity than biallelic genes. (the-scientist.com)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
  • Infinium data for four matched tumor-normal pairs and a dilution series of a tumor cell line mixed with its paired normal cell line are available in NCBI's Gene Expression Omnibus with accession [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976 GSE11976]. (lu.se)
  • The prostaglandin-endoperoxide synthase 2 gene (PTGS2), which encodes cyclooxygenase-2, was found to upregulate the expression of TGF-β2 ( 14 ). (spandidos-publications.com)
  • This gene encodes a member of the cysteine-aspartic acid protease (caspase) family. (cancerindex.org)
  • It is a single-copy gene, and encodes a proteolytically processed protein. (healthyguide.info)
  • Gene expression analysis is widely used in bioinformatics because it enables researchers to find gene products with increased or decreased synthesis in individuals with e.g. particular diseases. (knime.com)
  • Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. (ox.ac.uk)
  • Previous bioinformatics approaches were not predictive of new imprinted genes in the human term placenta. (ox.ac.uk)
  • Performed bioinformatics analysis of NGS data produced in the lab (RNA-seq, ChIP-seq), and developed algorithms and pipelines to address various biological questions: analysis of allelic imbalances in gene expression, chromatin marks signatures analysis using machine learning approaches and NGS experimental design. (netlify.app)
  • To construct a prognostic signature composed of DNA repair genes to effectively predict the prognosis of patients with head and neck squamous cell carcinoma (HNSCC). (frontiersin.org)
  • In the training set, 13 DNA repair genes were screened using univariate proportional hazard (Cox) regression analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis to construct a risk model, which was validated in the testing set. (frontiersin.org)
  • Several DNA repair genes have been confirmed to play an important role in the development and prognosis of HNSCC ( 5 - 7 ). (frontiersin.org)
  • Hence, constructing a risk model composed of DNA repair genes may be useful for predicting the prognosis of patients with HNSCC. (frontiersin.org)
  • In this study, we aimed to establish a prognostic prediction model for HNSCC based on DNA repair genes. (frontiersin.org)
  • The results showed that the risk model composed of DNA repair genes could effectively distinguish patients with different clinical outcomes and has independent predictive prognostic ability. (frontiersin.org)
  • One technique that is garnering wide attention in this realm is the DNA array, in which a number of different genes from an individual can be processed to look at certain genotypes. (medscape.com)
  • The specific effects that lead to inactivation of these pro-apoptotic or senescence pathways may impinge on major known tumor suppressors such as p53, but may also be due to effects on other genes and molecules within the p53 or other tumor suppressor pathways [ 5 ]. (biomedcentral.com)
  • We also investigated allelic imbalance (AI) in mammary carcinomas from (WKy x WF)F1 rats and Mcs7 heterozygous congenics. (mcw.edu)
  • The pattern of AI in carcinomas from both F1 and Mcs7 congenic rats was similar, suggesting a WF allelic loss. (mcw.edu)
  • In all, the analysis picked out 2,762 non-X-linked genes that fit the RAE pattern. (the-scientist.com)
  • Because setting a cutoff will cause the information loss, weighted gene co-expression networks are commonly used in biomedical analysis [ 12 ]. (biomedcentral.com)
  • We then perform a pathway enrichment analysis and look for compounds targeting the gene product of interest. (knime.com)
  • The user can investigate those genes and select genes of interest based on statistics from the gene expression analysis. (knime.com)
  • After quality control pruning, a total of 261 informative SNPs (214 genes) remained for analysis. (ox.ac.uk)
  • Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. (tamu.edu)
  • In order to further examine the possibility that PTPRD acts as a tumor suppressor gene in neuroblastoma, we initially analyzed the levels of PTPRD mRNA transcripts in a set of 88 neuroblastoma tumors using the R2: microarray analysis and visualization platform ( http://r2.amc.nl ) (University of Amsterdam). (biomedcentral.com)
  • Below we demonstrate an analysis where transcripts are grouped by their transcription start site (TSS), although gene-level or transcript-level analysis is also possible. (riken.jp)
  • Allelic Expression Imbalance Analysis Identified YAP1 Amplification in p53- Dependent Osteosarcoma. (cdc.gov)
  • A study identifies nearly 3,000 genes where one allele tends to be expressed more than the other, but the findings ignited controversy in the field. (the-scientist.com)
  • A change in one DNA nucleotide which may result in the substitution of one amino acid for another in a protein produced by a gene. (gene.vision)
  • The protein products of the three Ras genes are almost identical. (nature.com)
  • Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage. (nature.com)
  • What does this gene/protein do? (cancerindex.org)
  • What pathways are this gene/protein implicaed in? (cancerindex.org)
  • It sifts through the data of each cell's protein production to identify imbalances in the amount of different versions of the same protein. (sanger.ac.uk)
  • Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma. (biomedcentral.com)
  • The RS4939827 polymorphism in the SMAD7 GENE and its association with Mediterranean diet in colorectal carcinogenesis. (cdc.gov)
  • Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. (knime.com)
  • Investigate all statistically significant over/under expressed genes and select interesting ones by looking into their functional annotations. (knime.com)
  • We then cluster the genes based on similar expression profiles and investigate their biological pathways. (knime.com)
  • Genomic imprinting is an extreme form of allelic imbalance, in which the expression of imprinted genes is in a parent-of-origin dependent fashion. (xuwang.us)
  • By contrast, the 10 downregulated genes were primarily associated with epithelial membrane proteins ( 11 ). (spandidos-publications.com)
  • There are three Ras genes that generate four almost identical proteins: HRAS, NRAS, KRAS4A and KRAS4B [ 2 ]. (nature.com)
  • To tackle this issue, the development of network-based methods has become an effective tool in analyzing complex relationships among great number of entities such as genes and proteins. (biomedcentral.com)
  • Each of these allelic imbalance (AI) analyses takes into account the potentially heterogeneous amount of inferential uncertainty per sample, per feature (transcript, transcript-group, or gene), and per allele. (riken.jp)
  • Most of these databases provide at least the gene expression data for the samples contained in the project. (researchgate.net)
  • By testing on TCGA data, our novel method can provide more complete coverage of genes, more balanced module size and finer granularity than current methods in detecting modules with significant overall survival difference. (biomedcentral.com)
  • Today, we will demonstrate how to access all of these aforementioned data sources through the use case of analyzing and annotating gene expression data. (knime.com)
  • Hence, analyzing gene expression data directly is a straightforward way to find connections between genes and diseases. (knime.com)
  • In our data set, read counts for 10,542 genes were collected. (knime.com)
  • Hi, I have **RNA-seq data** and I am interested in whole gene expression results but also transcr. (usegalaxy.org)
  • Nye data tyder på at lungekreft som oppstår hos aldri-røykere bør ses på som en egen entitet, og dette vil kunne ha behandlingsmessige implikasjoner. (tidsskriftet.no)
  • Within RNA STAR, i turned on the option to include gene counts and so I included an hg38 GTF file from UCSC table browser. (usegalaxy.org)
  • RNA STAR said that of my 20 million total reads, 86% uniquely map (so 17 million reads uniquely mapping), however, when I take the sum of all the gene counts that RNA STAR outputs, it only adds up to 5 million reads. (usegalaxy.org)
  • My question is how come the total sum of all the gene counts doesn't add up to 17 million reads and why is it only 5 million? (usegalaxy.org)
  • How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? (lu.se)
  • Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. (ox.ac.uk)
  • None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. (ox.ac.uk)
  • In this vignette, we describe usage of a suite of tools, SEESAW , Statistical Estimation of allelic Expression using Salmon and Swish, which allow for testing allelic imbalance across samples. (riken.jp)
  • CRISPR-based screens are revolutionizing drug discovery as tools to identify genes whose ablation induces a phenotype of interest. (biomedcentral.com)
  • Gene panels to help identify subgroups at high and low risk of coronary heart disease among those randomized to antihypertensive treatment: the GenHAT study. (snpedia.com)
  • Genes mainly involved in coding adhesion molecules and growth factors have also been found to be upregulated in other types of CAFs, including colon ( 12 ) and pancreatic ( 13 ). (spandidos-publications.com)
  • BACKGROUND: Glyphosate resistance in Amaranthus palmeri is a result of amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene and increased expression of the target site of glyphosate, EPSP synthase (EPSPS). (usda.gov)
  • This study constructed a 13-DNA-repair-gene signature for the prognosis of HNSCC, which could accurately and independently predict the clinical outcome of the patient. (frontiersin.org)