• Cyclin F interacts with RRM2 to control the production of dNTPs in the cell to avoid genomic instability and frequency of mutations. (wikipedia.org)
  • Whole genome sequencing makes it possible to comprehensively discover the mutations, and the mutated genes, that are responsible for tumour formation. (nature.com)
  • Mutations in the CTNNB1 gene can cause a type of aggressive but noncancerous (benign) growth called a desmoid tumor. (medlineplus.gov)
  • CTNNB1 gene mutations are found in about 85 percent of all noninherited (sporadic) desmoid tumors. (medlineplus.gov)
  • The CTNNB1 gene mutations that cause desmoid tumors are somatic, which means they are acquired during a person's lifetime and are present only in tumor cells. (medlineplus.gov)
  • The CTNNB1 gene mutations that cause desmoid tumors usually occur in a region of the gene called exon 3. (medlineplus.gov)
  • Somatic mutations in the CTNNB1 gene are found in almost all pilomatricomas, a type of benign skin tumor associated with hair follicles. (medlineplus.gov)
  • The CTNNB1 gene mutations found in pilomatricomas are described as gain-of-function mutations. (medlineplus.gov)
  • Like pilomatricomas, pilomatrix carcinomas have somatic mutations in the CTNNB1 gene. (medlineplus.gov)
  • Mutations in the CTNNB1 gene have been found in Wilms tumor, a rare form of kidney cancer that occurs almost exclusively in children. (medlineplus.gov)
  • CTNNB1 gene mutations in Wilms tumor result in an overly active protein. (medlineplus.gov)
  • Despite a lack of previously reported NOTCH1 mutations, integrated analysis showed enrichments of alterations affecting Notch signaling in OTSCC. (biomedcentral.com)
  • We also observed somatic mutations in multiple therapeutically relevant genes, which may represent candidate drug targets in this highly lethal tumor type. (biomedcentral.com)
  • With the advent of NGS technique, the explosion of NGS data generated from the tumor tissues help researchers identify driver mutations in cancer-related genes, but relatively less attention is paid to the SNP data in healthy human populations when studying cancer. (biomedcentral.com)
  • By simply dividing the human genes into cancer-related genes and other genes, we compared the features of nonsynonymous, synonymous and nonsense mutations in these two gene sets from multiple aspects. (biomedcentral.com)
  • We provided lines of evidence that the nonsynonymous, synonymous and nonsense mutations in cancer-related genes undergo stronger purifying selection when compared to the expected pattern in other genes. (biomedcentral.com)
  • The synonymous SNPs, after excluding those in splicing regions, exhibit preferred changes in codon usage and higher codon frequencies in cancer-related genes compared to other genes, indicating the constraint exerted on these mutations. (biomedcentral.com)
  • Nonsense mutations are less frequent and located closer to stop codons in cancer-related genes than in other genes, which putatively minimize their deleterious effects. (biomedcentral.com)
  • Our study demonstrated the evolutionary constraint on mutations in CDS of cancer-related genes without the requirement of data from cancer tissues or patients. (biomedcentral.com)
  • Our work provides novel perspectives on interpreting the constraint on mutations in cancer-related genes. (biomedcentral.com)
  • We reveal extra constraint on synonymous mutations in cancer-related genes which is related to codon usage bias and is in addition to the splicing effect. (biomedcentral.com)
  • Thus, it is comparably important to study the role of synonymous mutations that affect the codon usage bias in cancer-related genes. (biomedcentral.com)
  • Loss-of-function mutations in APC or AXIN or activating mutations in the gene encoding β-catenin, CTNNB1 , lead to aberrant activation of Wnt/β-catenin signaling and have been causally linked to tumorigenesis of the colon, liver and skin [1] , [4] . (plos.org)
  • Although mutations in these same genes have not been observed as recurrent genetic events in breast tumors, there is strong evidence implicating Wnt/β-catenin activity in breast tumorigenesis. (plos.org)
  • Heterozygous missense mutations in the N-terminal motor or coiled-coil domains of the kinesin family member 5A (KIF5A) gene cause monogenic spastic paraplegia (HSP10) and Charcot-Marie-Tooth disease type 2 (CMT2). (kb.se)
  • These findings, together with the observation that many of the disease genes associated with amyotrophic lateral sclerosis disrupt cytoskeletal function and intracellular transport, led us to hypothesize that mutations in KIF5A are also a cause of amyotrophic lateral sclerosis. (kb.se)
  • We additionally show co-segregation with amyotrophic lateral sclerosis of two canonical splice-site mutations in two families. (kb.se)
  • Our pipeline, ExInAtor, identifies genes with excess load of somatic single nucleotide variants (SNVs) across panels of tumour genomes. (nature.com)
  • However, the frequency of such variants in patients who present with clinical disorders of pubertal development is currently unknown. (bvsalud.org)
  • DESIGN, SETTING AND PARTICIPANTS: We examined the sequence of MC3R in 362 adolescents with a clinical diagnosis of CDGP and 657 patients with nIHH, experimentally characterised the signalling properties of all non-synonymous variants found and compared their frequency to that in 5774 controls from a population-based cohort. (bvsalud.org)
  • Additionally, we established the relative frequency of predicted deleterious variants in individuals with self-reported delayed vs normally timed menarche/voice breaking in the UK Biobank cohort. (bvsalud.org)
  • Canonical GT-AG and non-canonical intron variants including AT-AC introns can coexist within the same gene, potentially with an effect on gene expression due to the slow removal of U12-type introns [ 10 ]. (biomedcentral.com)
  • Authors are encouraged to attempt these aneuploid analyses when reporting scRNA-seq data, much like copy-number variants are commonly reported in bulk genome sequencing data. (techscience.com)
  • These DNA primer pairs were designed by prioritizing the gene regions most commonly found in transcript variants. (bio-rad.com)
  • We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. (biomedcentral.com)
  • The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. (biomedcentral.com)
  • The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. (biomedcentral.com)
  • At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development. (biomedcentral.com)
  • Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants. (biomedcentral.com)
  • However, the known susceptibility variants are incompletely penetrant, many individuals who carry monogenic risk variants never develop PAH, and a subset of patients have deleterious variants in more than one risk gene. (biomedcentral.com)
  • Genetic analyses of larger cohorts using gene panels, exome sequencing (ES), or genome sequencing (GS) have further defined the frequency of individuals with deleterious variants in PAH risk genes and have identified novel candidate risk genes. (biomedcentral.com)
  • We performed a genome-wide association study (GWAS) and exome-sequencing analysis to identify common and rare genetic variants associated with plasma myeloperoxidase (MPO)-DNA complex levels, a biomarker for NETs, in the population-based Rotterdam Study cohort. (frontiersin.org)
  • We additionally performed exome-sequencing analysis in 960 individuals to investigate rare variants in candidate genes. (frontiersin.org)
  • Genome-wide association studies (GWAS) and exome-sequencing analysis have been successfully implemented as approaches to identify genetic variants associated with disease susceptibility. (frontiersin.org)
  • We performed additional in silico analyses to identify more evidence for the associated variants and genes in relation to the plasma MPO-DNA complex levels. (frontiersin.org)
  • Segregation analysis showed 66.6% (n = 3 for CNVs and n = 17 for SNVs) and 16.6% (n = 5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. (biomedcentral.com)
  • However, since then, studies using whole exome sequencing (WES) have evidenced sequence level contribution of de novo variants in the etiology of ASD and recent advancements in computational analyses of WES data suggests improvement in detection of copy number variants (CNVs) too. (biomedcentral.com)
  • PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
  • Based on pharmacological studies indicating a critical role of the mineralocorticoid receptor (MR) in the stress-induced bias toward dorsal striatal learning, we hypothesized that MR gene variants contribute to these individual differences. (eneuro.org)
  • Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been fully characterized. (cancerindex.org)
  • As a consequence of the economic interest in salmon, various genomic resources have been developed to identify genes and genomic mechanisms responsible for commercially important traits. (biomedcentral.com)
  • The results showed that USF1 significantly regulates 350 differentially expressed genes (DEGs). (spandidos-publications.com)
  • We predict several transcription factors to regulate differentially expressed genes between mLT-HSCs and other LT-HSC subsets. (biorxiv.org)
  • This example makes the CA of the codon frequencies in the coding sequences of Mycoplasma genitalium . (univ-lyon1.fr)
  • As a TF, USF1 has a bidirectional regulatory function, being able to regulate gene expression by activating or suppressing the promoter region of target genes ( 5 , 6 ). (spandidos-publications.com)
  • Once stabilized, β-catenin accumulates and translocates to the nucleus, where it complexes with TCF/LEF to activate transcription of target genes, such as MYC and CCND1 . (plos.org)
  • Fontsere C, de Manuel M, Marques-Bonet T, Kuhlwilm M. Admixture in mammals and how to understand its functional implications: on the abundance of gene flow in mammalian species, its impact on the genome, and roads into a functional understanding. (upf.edu)
  • Our analysis shows that ERBs upregulate canonical antiviral genes typical of mammalian systems, such as ISG15, IFIT1, and OAS3, yet demonstrate a remarkable lack of significant induction of proinflammatory genes classically implicated in primate filoviral pathogenesis, including CCL8, FAS, and IL6. (cdc.gov)
  • Whereas these cross-sectional analyses revealed potential biomarkers, they cannot control for the effects of the genetic heterogeneity underlying MS susceptibility required for a patient to develop MS and its potential influence on immune cell perturbations. (nature.com)
  • Here we conducted an in-depth pairwise analysis of the systemic immune compartment of 61 monozygotic twin pairs discordant for MS, in which both siblings carry the same genetic and early-life environmental risk for the disease, yet only one is affected by MS. This approach thus eliminated the majority of bias attributed to variable genetic and early environmental influences in a heterogenous population 17 , 18 . (nature.com)
  • This study aimed at identifying and selecting through partial diallel analysis, segregating populations of cowpea resistant to Macrophomina phaseolina and Thanatephorus cucumeris, based on the evaluation of general (GCA) and specific combining ability (SCA), involved in the genetic control of resistance. (geneticsmr.com)
  • Early genetic linkage and candidate gene studies indicated an autosomal dominant mode of inheritance for PAH risk. (biomedcentral.com)
  • These data suggest that additional genetic, epigenetic, environmental factors, and gene × environment interactions contribute to disease. (biomedcentral.com)
  • To understand the molecular-genetic basis of functional specialization and identify potential drug targets specific to each neuron subtype, we performed a genome wide assessment of both gene expression and splicing across EXC, PV, SST and VIP neurons from male and female mouse brains. (jneurosci.org)
  • Data from twin studies suggest a strong genetic role and a quantitative meta-analysis on all published twin studies in the context of ASD has estimated heritability component between 64 and 91% [ 9 ]. (biomedcentral.com)
  • An ectotherm's thermal tolerance is determined by both fixed genetic factors and plastic changes in behavior, morphology, physiology, and gene expression. (frontiersin.org)
  • Intense efforts to examine genetic alterations in human cancer have provided a catalogue of cancer-causing genes. (haematologica.org)
  • Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence. (cancerindex.org)
  • Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
  • G2/mitotic-specific cyclin-F is a protein that in humans is encoded by the CCNF gene. (wikipedia.org)
  • The protein encoded by this gene belongs to the Fbxs class and it was one of the first proteins in which the F-box motif was identified. (wikipedia.org)
  • SLBP is a protein that controls the mRNAs encoding canonical histones and H2A.X, thereby synchronizing histone metabolism with the cell cycle. (wikipedia.org)
  • The CTNNB1 gene provides instructions for making a protein called beta-catenin. (medlineplus.gov)
  • They cause the beta-catenin protein to be turned on all the time (constitutively active), which leads to the abnormal activation of certain genes. (medlineplus.gov)
  • Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. (mdpi.com)
  • The upregulated DEGs were primarily protein‑coding genes enriched in immune and inflammation response pathways, while the downregulated DEGs were mainly coding long non‑coding (lnc)RNAs, indicating the regulatory function of USF1. (spandidos-publications.com)
  • What does this gene/protein do? (cancerindex.org)
  • However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)
  • The gene EXO1 (exonuclease 1) was located at the 1q42 to q43 chromosomal region, a RAD2 nuclease family and encoding 846-amino acid protein [ 17 ]. (hindawi.com)
  • 5.0 × 10 −6 ) of SNPs annotated to four genes. (frontiersin.org)
  • In agreement with this, results from studies using salmon EST data as a source for SNP discovery show that when clustering EST-sequences into consensus sequences there is a high frequency of "SNPs" with heterozygote excess. (biomedcentral.com)
  • We produced assemblies for the five species ranging in aggregate length from 68 to 79 megabase pairs, identified putative orthologs for more than 12,000 human genes, and predicted more than 32,000 cross-species single nucleotide polymorphisms (SNPs). (biomedcentral.com)
  • Our new synergism-based method is useful for the identification of synergistic gene combinations in tumor development, and may expand our systemic understanding of a wide range of cancer-causing elements. (haematologica.org)
  • Mechanistically, EPB41L4A-AS2, acting at least in part as a tumor suppressor, upregulated tumor suppressor gene expression. (cancerindex.org)
  • Majority of the affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling. (biomedcentral.com)
  • Further, several GWAS candidates were regulatory genes that may participate in the regulation of stress responses, and gene ontologies related to development and morphogenesis were enriched, suggesting many of these genes influence thermal tolerance through effects on development and physiological status. (frontiersin.org)
  • The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. (biomedcentral.com)
  • Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). (biomedcentral.com)
  • To investigate the correlation between the polymorphism of estrogen receptor β gene (ESR2) rs3020450 and cancer susceptibility, and explore the epidemiological significance and the effect of ESR2 expression levels on the prognosis of ovarian cancer. (cancerindex.org)
  • The pooled analysis indicated no significant correlation between the ESR2 rs3020450 polymorphism and the cancer susceptibility. (cancerindex.org)
  • These results reveal numerous examples where neuron subtype-specific gene expression, as well as splice-isoform usage, can explain functional differences between neuron subtypes, including in presynaptic plasticity, postsynaptic receptor function, and synaptic connectivity specification. (jneurosci.org)
  • This analysis reveals numerous examples of neuron subtype-specific isoform usage with functional importance, identifies potential drug targets, and provides insight into the neuron subtypes involved in psychiatric disease. (jneurosci.org)
  • Functional analyses of transcripts showing alternative polyadenylation in response to salt show an enrichment in ABA signaling, and response to stresses such as salt or cadmium genes, among others. (upm.es)
  • We identified CCND3 and NRAS as cooperative genes with Bcl2 and Myc through the functional screening. (haematologica.org)
  • The study of functional synergism among cancer-causing genes is thus becoming one of the central issues in cancer research. (haematologica.org)
  • In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. (biomedcentral.com)
  • Despite this prototypical TCR repertoire gene usage, in recent years it has become apparent that there are variations within the iNKT cell repertoire that ultimately impact the antigen recognition capacity and consequently the functional outcomes during an immune response. (elifesciences.org)
  • 3 Interestingly, two BRCA1 haplotypes account for the bulk of the genotypes, the consensus at 59% frequency, and the most common non-consensus haplotype at 21% (fig 1). (bmj.com)
  • We identified 78 (1.3%) samples with non-canonical haplotypes, which in 62 cases were paired with a canonical haplotype. (bmj.com)
  • These algorithms estimate population haplotype frequencies from pooled SNP data and can make use of a list of the haplotypes that are known to exist in the population. (helsinki.fi)
  • Estimating population haplotype frequencies from pooled SNP data using incomplete prior information. (helsinki.fi)
  • Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. (lu.se)
  • Path analysis and canonical correlations for indirect selection of Jatropha genotypes with higher oil yield. (geneticsmr.com)
  • The selected pathways were used to design panels of real-time PCR primers tailored for the top-ranked genes for differential gene expression analysis. (bio-rad.com)
  • We used a genome-wide analysis which not only examined differential gene expression levels but could also detect differences in splice isoform usage. (jneurosci.org)
  • Proto-oncogene lncRNAs include HOTAIR, upregulated in multiple cancers, which recruits the repressive PRC2 chromatin regulatory complex to hundreds of genes 11 . (nature.com)
  • Since hundreds of genes are present on chromosome arms, high-quality inferences of aneuploidy can be made from scRNA-seq datasets. (techscience.com)
  • Thomson Reuters provided interactive pathway maps for 260 canonical pathways. (bio-rad.com)
  • It was also demonstrated that USF1 directly binds to the promoter region of 2,492 genes, which may be involved in the viral progression and cell proliferation pathways. (spandidos-publications.com)
  • Eukaryotic genes are transcribed as a primary transcript that is subsequently converted to a mature mRNA through several processing steps including splicing. (biomedcentral.com)
  • Splicing of introns is required for the expression of most eukaryotic genes. (biomedcentral.com)
  • We systematically violated canonical qPCR design ideas to develop a Pan-Degenerate Amplification and Adaptation (PANDAA), a degree mutation assay that mitigates the affect of sequence variation on probe-based qPCR efficiency. (floatingharborsyndrome.co.uk)
  • Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. (lu.se)
  • This strongly supports the amplification of E2F1 gene in predisposing to cancer. (biomedcentral.com)
  • Once in the nucleus, beta-catenin interacts with other proteins to control the activity (expression) of particular genes. (medlineplus.gov)
  • In these minor intron-containing genes (MIGs), the majority of introns are usually spliced by the major spliceosome, with only one or two introns being spliced by the minor spliceosome. (biomedcentral.com)
  • Both known and novel driver lncRNAs are distinguished by elevated gene length, evolutionary conservation and expression. (nature.com)
  • Gene expression signatures within memory B cells suggest qualitative differences in the antibody responses in aged patients with severe disease. (medrxiv.org)
  • Bio-Rad collaborated with Biogazelle, leaders in real-time PCR research, to design and experimentally validate PCR primers for gene expression assays across the human and mouse transcriptomes. (bio-rad.com)
  • Each gene target within a pathway was assigned a score based on the frequency of differential expression and its research significance. (bio-rad.com)
  • Reference genes are used in relative gene expression analysis to normalize for variation in the amount of input messenger RNA (mRNA) among samples. (bio-rad.com)
  • To ensure accurate quantitation, it is important to include one or more reference genes exhibiting constant expression levels under the experimental conditions. (bio-rad.com)
  • We provide a searchable web resource for exploring differential mRNA expression and splice form usage between excitatory, PV, SST, and VIP neurons ( http://research-pub.gene.com/NeuronSubtypeTranscriptomes ). (jneurosci.org)
  • This resource, combining a unique new dataset and novel application of analysis methods to multiple relevant datasets, identifies numerous potential drug targets for manipulating circuit function, reveals neuron subtype-specific roles for disease-linked genes, and is useful for understanding gene expression changes observed in human patient brains. (jneurosci.org)
  • Results Primary B cells exogenously expressing Bcl2 , Myc and Ccnd1 showed factor-independent growth ability, enhanced colony-forming capability and aggressive oncogenicity, unlike the cases observed with the expression of any combination of only two of the genes. (haematologica.org)
  • 7 Importantly, it is believed that other hitherto unknown genes also play important roles in lymphomagenesis in addition to the synergistic effects of the aforementioned two oncogenes since human B-cell lymphomas often show a variety of genes subject to alterations and/or deregulated expression. (haematologica.org)
  • Promoter region motif analysis indicated that ETV5 has more binding motifs and genes than USF1 itself for USF1‑regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. (spandidos-publications.com)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
  • How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? (lu.se)
  • Whole-genome linkage analysis and genome sequencing identified CCNF to be linked to both familial and sporadic ALS patients. (wikipedia.org)
  • We have presented a first catalogue of mutated lncRNA genes driving cancer, which will grow and improve with the application of ExInAtor to future tumour genome projects. (nature.com)
  • The Arabidopsis thaliana Niederzenz-1 genome sequence was recently published with an ab initio gene prediction. (biomedcentral.com)
  • Since non-canonical splice sites are difficult to predict ab initio, we checked for options to improve the annotation by transferring annotation information from the recently released Columbia-0 reference genome sequence annotation Araport11. (biomedcentral.com)
  • The improved gene set of the Nd-1 genome assembly (GeneSet_Nd-1_v1.1) was evaluated via comparison to the initial gene prediction (GeneSet_Nd-1_v1.0) as well as against Araport11 for the Col-0 reference genome sequence. (biomedcentral.com)
  • RNA-Seq data ("external hints") does not support the detection and annotation of non-canonical splice sites on genome sequence assemblies at a satisfying level [ 26 , 27 , 28 ]. (biomedcentral.com)
  • Each RBH couple consists of two genes, one from each of the two genome sequences (or genomes) to compare, which display the highest scoring hit in the other data set in a reciprocal manner [ 36 ]. (biomedcentral.com)
  • To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource - Rare Diseases Study. (biomedcentral.com)
  • Here, using the model species Drosophila melanogaster , we used a combination of Genome Wide Association mapping (GWAS) and transcriptomic profiling to characterize whether genes associated with thermal tolerance are primarily involved in dynamic stress responses or preparatory processes that influence physiological condition at the time of thermal stress. (frontiersin.org)
  • CCNF gene has 17 exons and is located at position 16p13.3 on the human chromosome. (wikipedia.org)
  • In depth analysis of the predicted gene set revealed some errors involving genes with non-canonical splice sites in their introns. (biomedcentral.com)
  • Incorporation of hints generated from Araport11 enabled the precise prediction of non-canonical splice sites. (biomedcentral.com)
  • Manual inspection of RNA-Seq read mapping and RT-PCR were applied to validate the structural annotations of non-canonical splice sites. (biomedcentral.com)
  • GeneSet_Nd-1_v1.1 contains previously missed non-canonical splice sites in 1256 genes. (biomedcentral.com)
  • Despite attempts to annotate non-canonical splice sites automatically [ 24 , 25 ], ab initio gene prediction without experimental support from e.g. (biomedcentral.com)
  • However, these reconstructions are prone to error caused by low quality of single-pass sequences, alternative splice forms, expressed pseudogenes and sequence similarities between transcripts within gene families. (biomedcentral.com)
  • We also apply our analysis to two other relevant datasets for comparison, and provide a searchable website for convenient access to the resource. (jneurosci.org)
  • By integrating these two datasets, 16 overlapped genes were detected, including downregulated lncRNA‑NEAT1 and upregulated TF‑ETV5. (spandidos-publications.com)
  • Using a stratified approach, we identify 15 high-confidence candidates: 9 novel and 6 known cancer-related genes, including MALAT1, NEAT1 and SAMMSON . (nature.com)
  • Downstream genes, including lncRNA‑NEAT1 and TF‑ETV5, may also have potential functions in the regulated network by USF1 and have potential functions in the progression of HCC. (spandidos-publications.com)
  • Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). (biomedcentral.com)
  • Here, we report computational and comparative analyses of survey sequence data to address the question of diversity. (biomedcentral.com)
  • Here is the example showing how you can search sequence data banks for gene sequences, compute the codon frequences for these genes, and perform a correspondence analysis (CA) of the frequencies table. (univ-lyon1.fr)
  • Cyclin F interacts with other proteins that are important for centrosomal duplication, gene transcription, and DNA synthesis, stability and repair. (wikipedia.org)
  • 10 Similarly, in recent studies, at least one third of genes in diverse organisms can exhibit alternative transcription, leading to the production of N-terminally extended proteins or alternative reading frames. (biorxiv.org)
  • Bioinformatics analysis revealed that several of the AS events could result in the production of novel tissue-specific proteins. (biomedcentral.com)
  • Such a transition has extensively deepened our knowledge on the function of driver genes and proteins and has provided a comprehensive understanding of the signaling networks occurring between cells, tissues, organs, and the entire organism. (molcells.org)
  • Importantly, these Notch pathway alterations were prognostic on multivariate analyses. (biomedcentral.com)
  • A complete of 109 hydatid cyst samples analyzed by PCR high-resolution melting (qPCR-HRM) curve of the cox1 gene, all isolates had been recognized as G1 genotype (sheep pressure). (floatingharborsyndrome.co.uk)
  • Of the few unusual haplotypes not in the canonical set, some are found in a genotype context that is similar to a genotype expected from a combination of a pair of canonical haplotypes, except that one or several polymorphic positions appear, unexpectedly, homozygous. (bmj.com)
  • A high proportion of OTSCCs also presented with alterations in drug targetable and chromatin remodeling genes. (biomedcentral.com)
  • Genomic alterations in DNA repair genes also play a substantial role in response to chemotherapeutics underlying the genetics of multiple cancers, including breast, colorectal, ovarian, and lung cancer [ 11 - 13 ]. (hindawi.com)
  • Based on meta-analysis the association between ESR2 rs3020450 polymorphism and cancer susceptibility was estimated and a case-control design was used to verify this result in ovarian cancer. (cancerindex.org)
  • In the stratified analysis by cancer types, significantly decreased risk was found in ovarian cancer (AG vs GG: OR = 0.73, 95%CI: 0.53-0.97, P = 0.03). (cancerindex.org)
  • Based on meta-analysis and case-control pooled results, ARP and PARP were evaluated respectively in allele (21.95% and7.97%), heterozygote (36.99% and 12.11%) and dominant model (36.84% and 12.97%) of rs3020450 polymorphism in ovarian cancer. (cancerindex.org)
  • These clusters of tentative consensus sequences (TCs) serve as a valuable resource for putative gene products. (biomedcentral.com)
  • One would expect that the large number of almost identical ohnologous sequences would make such gene transcript predictions particularly challenging in salmonid species. (biomedcentral.com)
  • Transcriptomics Reveal Antiviral Gene Induction in the Egyptian Rousette Bat Is Antagonized In Vitro by Marburg Virus Infection. (cdc.gov)
  • We combined the high-throughput of mass cytometry, facilitating the analysis of 57 twin pairs, with cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) of eight selected twin pairs to obtain a comprehensive overview of epitopes, transcriptome and T cell receptor (TCR) clonotypes. (nature.com)
  • In this approach, unphased SNP genotypes are compared to pairs of canonical haplotypes to identify potentially hemizygous regions. (bmj.com)
  • At the same time, the Frischauf laboratory also identified cyclin F as a new cyclin during their search for new candidate genes for polycystic kidney. (wikipedia.org)
  • Rare variant analysis of a large international consortium identified two new candidate genes- FBLN2 and PDGFD . (biomedcentral.com)
  • Candidate variant validation and parental segregation analysis was performed using orthogonal methods. (biomedcentral.com)
  • These results also have utility for directly comparing GWAS and transcriptomic approaches for identifying candidate genes associated with thermal tolerance. (frontiersin.org)
  • Outliers for F ST are candidate genes that may have experienced a history of natural selection in the Malawi lineage. (biomedcentral.com)
  • This vast population of uncharacterized genes likely includes many with novel roles in cancer. (nature.com)
  • We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. (lu.se)
  • The lower nonsynonymous to synonymous ratio observed in cancer-related genes suggests the suppression of amino acid substitutions in these genes. (biomedcentral.com)
  • Cancer was the top disease linked to the NET-associated genes. (frontiersin.org)
  • It is speculated that most cancers arise as a result of accumulation of altered cancer-causing genes. (haematologica.org)
  • This accounts for the fact that our knowledge about synergistic combinations of cancer-causing genes has remained limited. (haematologica.org)
  • Recent studies have demonstrated the existence of multiple copies of E2F1 gene in melanoma specimens which could explain the deregulated E2F1 activity in this type of cancer. (biomedcentral.com)
  • This is the first study that shows a relation between germline E2F1 CNV and melanoma, suggesting that altered copies of this gene might be a predisposing factor to skin cancer. (biomedcentral.com)
  • Here we identify CSNK1E , the gene encoding casein kinase 1 epsilon (CK1ε) as required specifically for the proliferation of breast cancer cells with activated β-catenin and confirm its role as a positive regulator of β-catenin-driven transcription. (plos.org)
  • FIP1 is a component of polyadenylation machinery, and mutation in this gene affects plant development, especially lateral root, cell division and elongation and response to different abiotic stresses. (upm.es)
  • Since U4atac snRNA is ubiquitously expressed, mutation in this gene is expected to result in systemic inhibition of the minor spliceosome. (biomedcentral.com)
  • Aneuploidy, the loss or gain of chromosome arms, appears less prevalent in normal tissue in these clonal mutant next-generation sequencing analyses. (techscience.com)
  • We report a computational and comparative analysis of these data that provides insight into the mechanisms that make closely related species different from one another. (biomedcentral.com)
  • Secondary, mRNA-seq analysis identified Gadd45 as a potential transcriptional target of dGLYAT, as depletion of dGLYAT decreased Gadd45 mRNA level. (sdbonline.org)
  • Gene fusions derived by transcriptional readthrough are driven by segmental duplication in human. (upf.edu)
  • Here, using colony-bred ERBs inoculated with a bat isolate of MARV, we use species-specific antibodies and an immune gene probe array (NanoString) to temporally characterize the transcriptional host response at sites of MARV replication relevant to primate pathogenesis and immunity, including CD14(+) monocytes/macrophages, critical immune response mediators, primary MARV targets, and skin at the inoculation site, where highest viral loads and initial engagement of antiviral defenses are expected. (cdc.gov)
  • Together, our matched-pair analysis of the extended twin approach allowed us to discern genetically and environmentally determined features of an MS-associated immune signature. (nature.com)
  • Contributors to severe MARV disease include immune response suppression and inflammatory gene dysregulation ('cytokine storm'), leading to systemic damage and often death. (cdc.gov)
  • Present high-risk HPV screening or analysis exams contain cytological or molecular methods principally based mostly on qualitative HPV DNA detection. (floatingharborsyndrome.co.uk)
  • E2F1, E2F2, and E2F3A are the three canonical activators of the E2F family of transcription factors. (wikipedia.org)
  • This gene encodes a member of the family of estrogen receptors and superfamily of nuclear receptor transcription factors. (cancerindex.org)
  • PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)
  • These genes increase the proliferation and differentiation of cells associated with the hair follicle matrix. (medlineplus.gov)
  • Pathway analysis of the identified genes showed their involvement in cellular development, molecular transport, RNA trafficking, cell-to-cell signaling and interaction, cellular growth and proliferation. (frontiersin.org)
  • These genes are transcriptionally deregulated as the partner genes of IgH translocation, and are thus thought to perform crucial roles in human B-cell lymphomagenesis. (haematologica.org)
  • Right here, we describe the event of a speedy quantitative polymerase chain response (qPCR) detection check of HPV16 and HPV18 oncogenes (E6 and E7) normalized on human gene encoding GAPDH. (floatingharborsyndrome.co.uk)
  • Most of the human SNP diversity at a given locus may be described as a set of "canonical" haplotypes, representing common haplotypes in a population. (bmj.com)
  • 2 A synergistic effect resulting from a combination of two genes from BCL2 , MYC and CCND1 has been implicated in human B-cell lymphomagenesis. (haematologica.org)
  • 7 That multiple genes are involved in human lymphoma formation has also been suggested by experimental mouse models. (haematologica.org)
  • 13 The identification and clarification of the multiple cooperative genes implicated in human lymphoma formation is important, although our present understanding of such genes remains scant. (haematologica.org)
  • The objective of this study was to identify additional cooperative gene(s) associated with BCL2 and MYC or MYC and CCND1 in human B-cell lymphomagenesis. (haematologica.org)
  • We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. (biorxiv.org)
  • Bioinformatic analysis of differential biology within the population of cells studied relies on inferences and grouping of cells due to the spotty nature of data within individual cell scRNA-seq gene counts. (techscience.com)
  • In this viewpoint, we direct investigators to select scRNA-seq CNA data analysis tools. (techscience.com)
  • Sequencing data will be deposited in a controlled access repository according to accepted standards and complete pathway analyses made available with the publication. (bmj.com)
  • C ) Summary data of frequency of MAIT tetramer-reactive cells among total TCRβ + cells pooled from two independent experiments, performed as in Panel B analyzing a total of 5-6 mice/group. (elifesciences.org)
  • The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the articles in buy nitrostat online without prescription this collection are only a starting point for conversations about a more sustainable future. (moragreekie.com)
  • Whole genomic DNA was extracted from every pattern and amplified for the presence of polymorphism within the mitochondrial cox1 gene of Echinococcus granulosus utilizing a excessive decision melting curve (HRM) methodology. (floatingharborsyndrome.co.uk)