Whole blood RNA-Seq data of Japanese CNO patients and healthy controls
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE187429 | GEO | 2021/11/05
REPOSITORIES: GEO
Similar Datasets
Project description:whole blood RNA-Seq data of Japanese CNO patients and healthy controls
| PRJNA777562 | ENA
Project description:Background
This work focuses on the computational modelling of osteomyelitis, a bone pathology caused by bacteria infection (mostly Staphylococcus aureus). The infection alters the RANK/RANKL/OPG signalling dynamics that regulates osteoblasts and osteoclasts behaviour in bone remodelling, i.e. the resorption and mineralization activity. The infection rapidly leads to severe bone loss, necrosis of the affected portion, and it may even spread to other parts of the body. On the other hand, osteoporosis is not a bacterial infection but similarly is a defective bone pathology arising due to imbalances in the RANK/RANKL/OPG molecular pathway, and due to the progressive weakening of bone structure.
Results
Since both osteoporosis and osteomyelitis cause loss of bone mass, we focused on comparing the dynamics of these diseases by means of computational models. Firstly, we performed meta-analysis on a gene expression data of normal, osteoporotic and osteomyelitis bone conditions. We mainly focused on RANKL/OPG signalling, the TNF and TNF receptor superfamilies and the NF-kB pathway. Using information from the gene expression data we estimated parameters for a novel model of osteoporosis and of osteomyelitis. Our models could be seen as a hybrid ODE and probabilistic verification modelling framework which aims at investigating the dynamics of the effects of the infection in bone remodelling. Finally we discuss different diagnostic estimators defined by formal verification techniques, in order to assess different bone pathologies (osteopenia, osteoporosis and osteomyelitis) in an effective way.
Conclusions
We present a modeling framework able to reproduce aspects of the different bone remodeling defective dynamics of osteomyelitis and osteoporosis. We report that the verification-based estimators are meaningful in the light of a feed forward between computational medicine and clinical bioinformatics
Model is encoded by Ruby and submitted and curated to BioModels by Ahmad Zyoud
2024-09-02 | BIOMD0000000923 | BioModels
Project description:RNA samples from the blood of patients with double tumors, single tumors and from healthy control subjects are studied by gene expression analysis using the whole genome microarray platform AB1700 from Applied Biosystems. Gene expression profiles are derived from the microarray raw data by biostatistical analysis. Differential gene expression between the study subgroups and categories is assessed: On the one hand, all possible pairwise comparisons between the subgroups A, B, C, D, E and N are made in order to elucidate characteristics of the individual subgroups. On the other hand, the higher-ranked categories “double cancer” (AB, consisting of subgroups A and B) and “single cancer” (category CDE, consisting of subgroups C, D and E) are compared to each other and to the normal controls (N). Finally, the category “double cancer” is compared to the different single cancer subgroups (C, D and E). Analysis on the level of the higher ranked categories “double cancer” and “single cancer” aims at identifying the common traits of patients who have developed two independent tumors, as opposed to patients with only one tumor entity and to healthy individuals. Based on the functional annotation of the induced and repressed genes found in these comparisons, biological processes and pathways which are differentially activated in the subgroups or categories are identified, thus providing insights into their molecular characteristics. Furthermore, gene expression data are used to derive classifier rules, which are aimed at discriminating subjects from the different subgroups and categories and may constitute the basis for a future diagnostic classification tool. Keywords: microarray analysis, double-single primary malignancies A total of 66 individuals were analyzed:The primary study group consisted of 24 patients with two primary malignancies (group AB) (one of the primaries being of the breast, colon or ovary). The four control groups consisted of a total of 33 single cancer patiens: 10 with colon cancer (group C), 14 with breast cancer (group D), 9 with ovarian cancer (group E_) and 10 healthy individuals (group N). 4 samples (GECM-061_14, GECM-061_37, GECM-061_54 and GECM-061_72) were identifed as outliers by MA plots and therfore they were excluded from the study.
| S-ECPF-GEOD-11545 | biostudies-other
Project description: Not available
| S-BSST1655 | biostudies-other
Project description:We sought to utilize disease discordant twins and a novel viral-human gene microarray assay using whole human genome microarray in combination with a set of over 6,000 probes, which correspond to the majority of known viral genesrole of shared viral infections and the activation of shared antiviral signaling pathways in the development of SAID
2016-06-20 | GSE74027 | GEO
Project description:PURPOSE:The aim of this multicenter trial was to generate a [123I]FP-CIT SPECT database of healthy controls from the common SPECT systems available in Japan. METHODS:This study included 510 sets of SPECT data from 256 healthy controls (116 men and 140 women; age range, 30-83 years) acquired from eight different centers. Images were reconstructed without attenuation or scatter correction (NOACNOSC), with only attenuation correction using the Chang method (ChangACNOSC) or X-ray CT (CTACNOSC), and with both scatter and attenuation correction using the Chang method (ChangACSC) or X-ray CT (CTACSC). These SPECT images were analyzed using the Southampton method. The outcome measure was the specific binding ratio (SBR) in the striatum. These striatal SBRs were calibrated from prior experiments using a striatal phantom. RESULTS:The original SBRs gradually decreased in the order of ChangACSC, CTACSC, ChangACNOSC, CTACNOSC, and NOACNOSC. The SBRs for NOACNOSC were 46% lower than those for ChangACSC. In contrast, the calibrated SBRs were almost equal under no scatter correction (NOSC) conditions. A significant effect of age was found, with an SBR decline rate of 6.3% per decade. In the 30-39 age group, SBRs were 12.2% higher in women than in men, but this increase declined with age and was absent in the 70-79 age group. CONCLUSIONS:This study provided a large-scale quantitative database of [123I]FP-CIT SPECT scans from different scanners in healthy controls across a wide age range and with balanced sex representation. The phantom calibration effectively harmonizes SPECT data from different SPECT systems under NOSC conditions. The data collected in this study may serve as a reference database.
| S-EPMC5993845 | biostudies-literature
Project description:There is no scientific consensus that a relationship exists between the ABO blood group and personality traits. However, a recent study hypothesized that the dopamine beta-hydroxylase (DBH) gene is in linkage with the ABO gene. The sample population consisted of 1,427 healthy Japanese subjects who completed the Temperament and Character Inventory (TCI). Each subject's ABO blood type was determined by genotyping the rs8176719 and rs8176746 ABO gene single-nucleotide polymorphisms (SNPs) using a TaqMan genotyping assay. The relationships between the six ABO genotypes or four ABO phenotypes and personality traits were examined using a multivariate analysis of covariance (MANCOVA), controlling for age and sex. The MANCOVA data showed a significant difference in TCI scores among the ABO genotype groups (F [7, 1393] = 3.354, p = 0.001). A subsequent univariate analysis showed a significant difference in the mean scores for Persistence among the genotype groups (F = 2.680, partial η2 = 0.010, p = 0.020). Similarly, dividing the ABO blood type into four phenotypes revealed a significant difference among the phenotype groups (F [7, 1397] = 2.529, p = 0.014). A subsequent univariate analysis showed a significant difference among the phenotype groups in the mean scores for Persistence (F = 2.952, partial η2= 0.006, p = 0.032). We observed a significant association between ABO blood group genotypes and personality traits in a large number of healthy Japanese subjects. However, these results should be regarded as preliminary and should be interpreted with caution because it is possible that the association between ABO blood group genotype and the Persistence trait is relatively weak.
| S-EPMC4433257 | biostudies-literature
Project description:Investigating differential gene expression between clinical phenotypes in primary Sjögren's Syndrome using matched healthy controls as a further comparator group. Samples are derived from the UK Primary Sjögren's Syndrome Registry (UKPSSR)
2019-09-30 | E-MTAB-8277 | biostudies-arrayexpress
Project description:Staphylococcus aureus is the principal causative agent of osteomyelitis, a serious bacterial infection of bone that is associated with progressive inflammatory damage. Bone-forming osteoblasts have increasingly been recognized to play an important role in the initiation and progression of detrimental inflammation at sites of infection, and have been demonstrated to release an array of inflammatory mediators and factors that promote osteoclastogenesis and leukocyte recruitment following bacterial challenge. In the present study, we describe elevated bone tissue levels of the potent neutrophil-attracting chemokines, CXCL1, CXCL2, CXCL3, CXCL5, CCL3, and CCL7, in a murine model of post-traumatic staphylococcal osteomyelitis. RNA-Seq gene ontology analysis of isolated primary murine osteoblasts showed enrichment in differentially expressed genes involved in cell migration and chemokine receptor binding and chemokine activity following S. aureus infection, and a rapid increase in the expression of mRNA encoding CXCL1, CXCL2, CXCL3, CXCL5, CCL3, and CCL7, in these cells. Importantly, we have confirmed that such upregulated gene expression results in protein production with the demonstration that S. aureus challenge elicits the rapid and robust release of these chemokines by osteoblasts and does so in a bacterial dose-dependent manner. Furthermore, we have confirmed the ability of soluble osteoblast-derived chemoattractants to elicit the migration of a neutrophil-like cell line. As such, these studies demonstrate the robust production of CXCL1, CXCL2, CXCL3, CXCL5, CCL3, and CCL7, by osteoblasts in response to S. aureus infection, and the release of such neutrophil-attracting chemokines provides an additional mechanism by which osteoblasts could drive the inflammatory bone loss associated with staphylococcal osteomyelitis.
2022-11-12 | GSE217455 | GEO
Project description:We report RNA-Seq data obtained from nucleus accumbens tissue of HDID-1 mice subjected to chronic stimulation via CNO/DREADDs within a Drinking in The Dark (DID) Paradigm. Here, we found that chronically increasing NAc activity (via CNO/hM3Dq) decreased binge-like drinking, an effect lasting for at least 7 days . CNO did not alter intake in hM4Di- or GFP-expressing mice. We observed interesting and significant changes in expression of several plasticity-related genes (e.g. Hdac4 was increased with binge drinking, and ameliorated with CNO).
2019-06-21 | GSE133115 | GEO