scholarly journals Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder

2009 ◽  
Vol 85 (1) ◽  
pp. 13-24 ◽  
Author(s):  
Peter Holmans ◽  
Elaine K. Green ◽  
Jaspreet Singh Pahwa ◽  
Manuel A.R. Ferreira ◽  
Shaun M. Purcell ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Gene Ontology ◽  
Study Data ◽  
Data Sets ◽  
Gene Ontology Analysis

Analysis of Transcriptomic Similarity between Osteosarcoma Cell Lines and Primary Tumors

Oncology ◽  
2020 ◽  
Vol 98 (11) ◽  
pp. 814-816
Author(s):  
Sai Batchu ◽  
Justin Lee Gold
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Cell Lines ◽  
Disease Process ◽  
Published Data ◽  
Data Sets ◽  
Osteosarcoma Cell ◽  
Gene Ontology Analysis ◽  
Primary Tumors

<b><i>Background:</i></b> Osteosarcoma (OS) cell lines are commonly used to mimic tumors for in vitro experiments. The present study explores the resemblance of OS cell lines to OS primary tumors in regard to gene expression. <b><i>Methods:</i></b> Transcriptomic data were retrieved from published data sets for 18 primary tumor samples and 13 commonly used OS cell lines. Tumor purity was accounted for when correlating tumor and cell line gene expression. Differentially expressed genes between tumors and cell lines were discovered and gene ontology analysis was performed. <b><i>Results:</i></b> Certain commonly used cell lines, including NY, NOS1, and U2OS, display less resemblance to OS tumors than do other cell lines. For genes overexpressed in tumors, and consequently underexpressed in cell lines, gene ontology analysis enriched pathways related to cell-cell adhesion and stimulus detection. <b><i>Conclusion:</i></b> The pathways dysregulated between cell lines and tumors have been implicated in OS pathogenesis. Therefore, the findings suggest that the transcriptome of OS cell lines may not be completely representative of OS primary tumors’ gene expression and the disease process.

scholarly journals COVID-19 in patients undergoing chronic kidney replacement therapy and kidney transplant recipients in Scotland: findings and experience from the Scottish renal registry

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Samira Bell ◽  
◽  
Jacqueline Campbell ◽  
Jackie McDonald ◽  
Martin O’Neill ◽  
...  
Keyword(s):  
Public Health ◽  
Replacement Therapy ◽  
Study Data ◽  
Data Sets ◽  
Kidney Transplant Recipients ◽  
The Public ◽  
Transplant Patients ◽  
Kidney Replacement Therapy ◽  
Observational Cohort ◽  
Respiratory Coronavirus

Abstract Background Infection with the severe acute respiratory coronavirus 2 (SARS-CoV-2) has led to a worldwide pandemic with coronavirus disease 2019 (COVID-19), the disease caused by SARS-CoV-2, overwhelming healthcare systems globally. Preliminary reports suggest a high incidence of infection and mortality with SARS-CoV-2 in patients receiving kidney replacement therapy (KRT). The aims of this study are to report characteristics, rates and outcomes of all patients affected by infection with SARS-CoV-2 undergoing KRT in Scotland. Methods Study design was an observational cohort study. Data were linked between the Scottish Renal Registry, Health Protection Scotland and the Scottish Intensive Care Society Audit Group national data sets using a unique patient identifier (Community Health Index (CHI)) for each individual by the Public Health and Intelligence unit of Public Health, Scotland. Descriptive statistics and survival analyses were performed. Results During the period 1st March 2020 to 31st May 2020, 110 patients receiving KRT tested positive for SARS-CoV-2 amounting to 2% of the prevalent KRT population. Of those affected, 86 were receiving haemodialysis or peritoneal dialysis and 24 had a renal transplant. Patients who tested positive were older and more likely to reside in more deprived postcodes. Mortality was high at 26.7% in the dialysis patients and 29.2% in the transplant patients. Conclusion The rate of detected SARS-CoV-2 in people receiving KRT in Scotland was relatively low but with a high mortality for those demonstrating infection. Although impossible to confirm, it appears that the measures taken within dialysis units coupled with the national shielding policy, have been effective in protecting this population from infection.

Genome-wide screening of m6A-modified transcript in the Wilms’ tumor

2021 ◽  
Author(s):  
Zhuo Liu ◽  
Feng He ◽  
Jing Liu ◽  
Shengrong OuYang ◽  
Zexi Li ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Real Time ◽  
Real Time Pcr ◽  
Wilms Tumor ◽  
Expression Patterns ◽  
Mrna Levels ◽  
Gene Ontology Analysis ◽  
Quantitative Real Time Pcr ◽  
Related Factors ◽  
Significant Difference

Abstract Background Wilms’ tumor, also called nephroblastoma, is the most common pediatric renal malignancy. The pathogenesis of Wilms’ tumor has been attributed to several genetic and epigenetic factors. However, the most pervasive internal mRNA modification that affects almost every process of RNA metabolism, RNA N6-Methyladenosine (m6A) methylation, has not been characterized in Wilms’ tumor. Methods Wilms’ tumor (WT) and adjacent non-cancerous (NC) tissue samples were obtained from 23 children with nephroblastoma, and the global m6A levels were measured by mass spectrometry. Analyses by m6A-mRNA epitranscriptomic microarray and mRNA microarray were performed, and m6A-related mRNAs were validated by quantitative real-time PCR for input and m6A-immunoprecipitated RNA samples from WT and NC tissues. Gene ontology analysis and KEGG pathway analysis were performed for differentially expressed genes, and expression of RNA methylation-related factors was measured by quantitative real-time PCR. Results The total m6A methylation levels in total RNA of WT samples and NC samples were (0.21 ± 0.01)% and (0.22 ± 0.01)%, respectively, with no statistically significant difference. Fifty-nine transcripts were differentially m6A-methylated between the WT and NC groups, which showed distinct m6A modification patterns. Gene ontology analysis indicated that m6A-modified genes were enriched in cancer-associated pathways, including the mTOR pathway, and conjoint analysis of the unique methylation and gene expression patterns in WT samples suggested an association with metabolic pathways.The mRNA levels of the m6A-related “reader” genes, YTHDF1, YTHDF2 and IGF2BP3, were statistically higher in WT samples than in NC samples. Conclusion This is the first study to determine the m6A modification profiles in Wilms’ tumor. Our data provide novel information regarding patterns of m6A modification that correlate with carcinogenesis in Wilms’ tumor.

Abstract P112: Elevated Blood Pressure In Conventionalized Germ-free Rats Is Coupled With Upregulation Of Kynurenic Pathway Metabolites And Central Immune Responses

Hypertension ◽  
2020 ◽  
Vol 76 (Suppl_1) ◽  
Author(s):  
Tao Yang ◽  
Saroj Chakraborty ◽  
Piu Saha ◽  
Blair Mell ◽  
Xi Cheng ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Gene Ontology ◽  
Synaptic Plasticity ◽  
Cell Differentiation ◽  
Gut Microbiota ◽  
Immune Responses ◽  
Kynurenic Acid ◽  
Gene Ontology Analysis ◽  
Germ Free ◽  
Sd Rats

Background: Recent evidence supports that metabolic dysfunction underlies hypertension. Injection of kynurenate, a metabolite of tryptophan pathway, into the paraventricular nucleus of the hypothalamus (PVN) lowers blood pressure (BP). Intestinal absorption and metabolism of tryptophan are impacted by gut microbiota. Since gut-brain axis contributes to gut dysbiosis-inducd hypertension, we hypothesized that gut microbiota modulates the levels of kynurenic pathway metabolites that have central impact on BP regulation. Methods: We, for the first time, used 7 weeks old male Germ-free (GF) Spague Dawley (SD) rats (n=5) and GF rats co-housed with conventional SD rats for 10 days (GFC) (n=6). BP was measured by tail-cuff. Serum metabolites were quantified by 6495 triple quandrople mass spectrometryand data was normalized using isotoplic labelled compounds. The nucleus of the solitary tract (NTS), the principal sensory nucleus for peripheral changes, and the PVN, a relay center projecting sympathetic output based on the integrated afferent inputs from brain regions including NTS, were analyzed by microarray hybridization for mRNA expression. Results: Compared to the GF rats, GFC rats had significantly higher systolic (139 mmHg vs 115 mmHg, p <0.05), diastolic BP (96 mmHg vs 79 mmHg, p <0.05), and serum levels of kynurenic acid (-9.76 vs -10.21, p <0.05) and 3-hydroxy kynurenine (-6.49 vs -7.34, p <0.01). Coupled with these increases in kynurenic pathway metabolites, microarray analyses demonstrated increased immune responses (e.g. Cd74, Il1b, Cxcl1, Mmp14 ) in the PVN (gene ontology analysis, p <0.001) and increased cell differentiation and synaptic plasticity (e.g. Sox11, Tp53, Cdk6, Hoxb4, Foxo4, Cyr61 ) in the NTS (gene ontology analysis, p <0.01). Conclusion: Colonization of gut microbiota in GF rats induced increased cell differentiation and synaptic plasticity in the NTS and immune responses in the PVN, indicating the restructured sensory neurons of the NTS and enhanced sympathetic output from the PVN. These are in line with increased levels of kynurenic acid and 3-hydroxy kynurenine, and BP, respectively, suggesting that BP regulation by the gut-brain axis may be mediated by kynurenic pathway.

Comparative analysis of microRNA expression profiles in the colons of specific pathogen-free mice and germ-free mice

2021 ◽  
Author(s):  
Ayako Aoki ◽  
Reiji Aoki ◽  
Madoka Yatagai ◽  
Toshiyuki Kawasumi
Keyword(s):  
Gene Ontology ◽  
Comparative Analysis ◽  
Expression Profiles ◽  
Microrna Expression ◽  
Gene Ontology Analysis ◽  
Specific Pathogen Free ◽  
Germ Free ◽  
Mrna Targets ◽  
Significant Gene ◽  
Specific Pathogen

ABSTRACT MicroRNAs play an important role in microbiota–host crosstalk. In this study, we compared microRNA expression in whole colons of specific pathogen-free mice and germ-free mice. Forty-eight microRNAs were differentially expressed by more than 2-fold. Gene ontology analysis of the predicted mRNA targets revealed that the majority of the most significant gene ontology terms were related to GTPases and nerves.

scholarly journals hnRNP A1 Regulates Alternative Splicing of Tau Exon 10 by Targeting 3′ Splice Sites

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 936 ◽  
Author(s):  
Yongchao Liu ◽  
Donggun Kim ◽  
Namjeong Choi ◽  
Jagyeong Oh ◽  
Jiyeon Ha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Alternative Splicing ◽  
Splice Site ◽  
Hnrnp A1 ◽  
Gene Ontology Analysis ◽  
Splice Sites ◽  
Neuronal Function ◽  
Brain Functions ◽  
Exon 10

The ratio control of 4R-Tau/3R-Tau by alternative splicing of Tau exon 10 is important for maintaining brain functions. In this study, we show that hnRNP A1 knockdown induces inclusion of endogenous Tau exon 10, conversely, overexpression of hnRNP A1 promotes exon 10 skipping of Tau. In addition, hnRNP A1 inhibits splicing of intron 9, but not intron 10. Furthermore, hnRNP A1 directly interacts with the 3′ splice site of exon 10 to regulate its functions in alternative splicing. Finally, gene ontology analysis demonstrates that hnRNP A1-induced splicing and gene expression targets a subset of genes with neuronal function.

scholarly journals ExAtlas: An interactive online tool for meta-analysis of gene expression data

2015 ◽  
Vol 13 (06) ◽  
pp. 1550019 ◽  
Author(s):  
Alexei A. Sharov ◽  
David Schlessinger ◽  
Minoru S. H. Ko
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Gene Expression Data ◽  
Fixed Effects ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Data Sets ◽  
Expression Data ◽  
Gene Set ◽  
Public Data

We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g. all gene expression profiles versus all Gene Ontology annotations). ExAtlas handles both users’ own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher’s methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pairwise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and three-dimensional images. Some of the most widely used public data sets (e.g. GNF/BioGPS, Gene Ontology, KEGG, GAD phenotypes, BrainScan, ENCODE ChIP-seq, and protein–protein interaction) are pre-loaded and can be used for functional annotations.

Sign in / Sign up

Export Citation Format

Share Document