Similarities and differences between exome sequences found in a variety of tissues from the same individual.
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ABSTRACT:
SUBMITTER: Gomez-Ramos A
PROVIDER: S-EPMC4077829 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:By combining transcriptomic data with other data sources, inferences can be made about functional changes during ageing. Thus, we conducted a meta-analysis on 127 publicly available microarray and RNA-Seq datasets from mice, rats and humans, identifying a transcriptomic signature of ageing across species and tissues. Analyses on subsets of these datasets produced transcriptomic signatures of ageing for brain, heart and muscle. We then applied enrichment analysis and machine learning to functionally describe these signatures, revealing overexpression of immune and stress response genes and underexpression of metabolic and developmental genes. Further analyses revealed little overlap between genes differentially expressed with age in different tissues, despite ageing differentially expressed genes typically being widely expressed across tissues. Additionally we show that the ageing gene expression signatures (particularly the overexpressed signatures) of the whole meta-analysis, brain and muscle tend to include genes that are central in protein-protein interaction networks. We also show that genes underexpressed with age in the brain are highly central in a co-expression network, suggesting that underexpression of these genes may have broad phenotypic consequences. In sum, we show numerous functional similarities between the ageing transcriptomes of these important tissues, along with unique network properties of genes differentially expressed with age in both a protein-protein interaction and co-expression networks.
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Project description:Human synovial joints display a characteristic anatomic distribution of arthritis, e.g. rheumatoid arthritis primarily affects the metacarpophalangeal and proximal finger joints, but rarely the distal finger joints, whereas osteoarthritis occurs in the distal and proximal finger joints. Pelvospondylitis has a selective localization to the spine and sacroiliac joints. Is this tropism due to differences between the cartilages at the molecular level? To substantiate this concept the present study provides a background detailed compositional analysis by relative quantification of extracellular matrix proteins in articular cartilages, meniscus, intervertebral disc, rib, and tracheal cartilages on samples from 5-6 different individuals using an optimized approach for proteomics. Tissue extraction followed by trypsin digestion and two-dimensional LC separations coupled to tandem mass spectrometry, relative quantification with isobaric labeling, iTRAQ(TM), was used to compare the relative abundance of about 150 proteins. There were clear differences in protein patterns between different kinds of cartilages. Matrilin-1 and epiphycan were specific for rib and trachea, whereas asporin was particularly abundant in the meniscus. Interestingly, lubricin was prominent in the intervertebral disc, especially in the nucleus pulposus. Fibromodulin and lumican showed distributions that were mirror images of one other. Analyses of the insoluble residues from guanidine extraction revealed that a fraction of several proteins remained unextracted, e.g. asporin, CILP, and COMP, indicating cross-linking. Distinct differences in protein patterns may relate to different tissue mechanical properties, and to the intriguing tropism in different patterns of joint pathology.
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Project description:Arbovirus can cause diseases with a broad spectrum from mild to severe and long-lasting symptoms, affecting humans worldwide and therefore considered a public health problem with global and diverse socio-economic impacts. Understanding how they spread within and across different regions is necessary to devise strategies to control and prevent new outbreaks. Complex network approaches have widespread use to get important insights on several phenomena, as the spread of these viruses within a given region. This work uses the motif-synchronization methodology to build time varying complex networks based on data of registered infections caused by Zika, chikungunya, and dengue virus from 2014 to 2020, in 417 cities of the state of Bahia, Brazil. The resulting network sets capture new information on the spread of the diseases that are related to the time delay in the synchronization of the time series among different municipalities. Thus the work adds new and important network-based insights to previous results based on dengue dataset in the period 2001-2016. The most frequent synchronization delay time between time series in different cities, which control the insertion of edges in the networks, ranges 7 to 14 days, a period that is compatible with the time of the individual-mosquito-individual transmission cycle of these diseases. As the used data covers the initial periods of the first Zika and chikungunya outbreaks, our analyses reveal an increasing monotonic dependence between distance among cities and the time delay for synchronization between the corresponding time series. The same behavior was not observed for dengue, first reported in the region back in 1986, either in the previously 2001-2016 based results or in the current work. These results show that, as the number of outbreaks accumulates, different strategies must be adopted to combat the dissemination of arbovirus infections.
| S-EPMC9980430 | biostudies-literature
Project description:We compare, in human macrophages, stimuli considered to induce M1 or M2 type of activation, also termed classical and alternative activation. This dataset highlights key differences between the M1 and M2 stimuli pointing to the need of a revision of the paradigm. Macrophages were left untreated or stimulated with IL-4 and IL-13 (prototypic M1 stimuli), Dexamethasone (Glucocorticoid receptor agonist) which has been hitherto considered M2, IL-10 which also falls under the M2 umbrella, and LPS and Interferon Gamma considered M1 stimuli.
2014-01-03 | GSE51446 | GEO
Project description:The human AA dataset 5 includes the gene expression profile of monocyte-derived macrophages isolated from blood donor buffy coats and plated on TCP in medium containing 10% autologous serum. Cells were stimulated for 120 hours with 50 ng/ml of IL-4, 50 U/ml of IFN-γ plus 12.5 ng/ml of TNF-α, 50 ng/ml of M-CSF or 50 ng/ml of IL-10. RNA samples were isolated using TriPure isolation reagent (Roche) and the RNeasy Mini Kit-Qiagen Clean up method. The transcriptional profile was evaluated in two independent cell preparations, each derived from a different single donor using the HT12 V4 R2 bead chip arrays from Illumina.
2013-07-26 | GSE49240 | GEO
Project description:Background & aimsGastroparesis can be diabetic or idiopathic, yet little is known about differences in their presentation. We compared clinical characteristics, symptoms, and gastric emptying in patients with type 1 or type 2 diabetic (DG) or idiopathic (IG) gastroparesis.MethodsWe analyzed data from 416 patients with gastroparesis who were enrolled in the National Institute of Diabetes and Digestive and Kidney Diseases Gastroparesis Registry; 254 had IG (most were female and white), and 137 had DG (78 had type 1 and 59 had type 2). Registry data included detailed histories, physical examinations, results from gastric emptying scintigraphy, and responses to validated symptom questionnaires.ResultsPatients with type 2 diabetes mellitus (DM) were an average of 13 years older at the onset of symptoms of gastroparesis and heavier than patients with IG. Patients with type 1 DM had more hospitalizations in the past year than patients with IG. Symptoms that prompted evaluation more often included vomiting for DG and abdominal pain for IG. Patients with DG had more severe retching and vomiting than those with IG, whereas patients with IG had more severe early satiety and postprandial fullness subscores. Compared with IG, gastric retention was greater in patients with type 1 DM. More than 50% of patients with type 1 DM had severe retention (>35% at 4 hours); they took prokinetic agents more frequently and were more likely to receive gastric electric stimulation.ConclusionsThere are similarities and differences in clinical characteristics of DG and IG. Gastroparesis is a heterogeneous disorder; its etiology affects symptoms and severity. Long-term studies are needed to determine whether the differences in symptoms and gastric emptying affect progression and treatment responses.
| S-EPMC3499102 | biostudies-literature
Project description:Spondyloarthritis (SpA) encompasses a broad spectrum of conditions occurring from childhood to middle age. Key features of SpA include axial and peripheral arthritis, enthesitis, extra-articular manifestations, and a strong association with HLA-B27. These features are common across the ages but there are important differences between juvenile and adult onset disease. Juvenile SpA predominantly affects the peripheral joints and the incidence of axial arthritis increases with age. Enthesitis is important in early disease. This review article highlights the similarities and differences between juvenile and adult SpA including classification, pathogenesis, clinical features, imaging, therapeutic strategies, and disease outcomes. In addition, the impact of the biological transition from childhood to adulthood is explored including the importance of musculoskeletal and immunological maturation. We discuss how the changes associated with adolescence may be important in explaining age-related differences in the clinical phenotype between juvenile and adult SpA and their implications for the treatment of juvenile SpA.
| S-EPMC8200411 | biostudies-literature
Project description:The human AA dataset 5 includes the gene expression profile of monocyte-derived macrophages isolated from blood donor buffy coats and plated on TCP in medium containing 10% autologous serum. Cells were stimulated for 120 hours with 50 ng/ml of IL-4, 50 U/ml of IFN-γ plus 12.5 ng/ml of TNF-α, 50 ng/ml of M-CSF or 50 ng/ml of IL-10. RNA samples were isolated using TriPure isolation reagent (Roche) and the RNeasy Mini Kit-Qiagen Clean up method. The transcriptional profile was evaluated in two independent cell preparations, each derived from a different single donor using the HT12 V4 R2 bead chip arrays from Illumina. Total RNA obtained from monocyte-derived macrophages exposed to representative polarizing cytokines
2013-07-26 | E-GEOD-49240 | biostudies-arrayexpress
Project description:BackgroundAstrocytomas are the most common primary brain tumors distinguished into four histological grades. Molecular analyses of individual astrocytoma grades have revealed detailed insights into genetic, transcriptomic and epigenetic alterations. This provides an excellent basis to identify similarities and differences between astrocytoma grades.MethodsWe utilized public omics data of all four astrocytoma grades focusing on pilocytic astrocytomas (PA I), diffuse astrocytomas (AS II), anaplastic astrocytomas (AS III) and glioblastomas (GBM IV) to identify similarities and differences using well-established bioinformatics and systems biology approaches. We further validated the expression and localization of Ang2 involved in angiogenesis using immunohistochemistry.ResultsOur analyses show similarities and differences between astrocytoma grades at the level of individual genes, signaling pathways and regulatory networks. We identified many differentially expressed genes that were either exclusively observed in a specific astrocytoma grade or commonly affected in specific subsets of astrocytoma grades in comparison to normal brain. Further, the number of differentially expressed genes generally increased with the astrocytoma grade with one major exception. The cytokine receptor pathway showed nearly the same number of differentially expressed genes in PA I and GBM IV and was further characterized by a significant overlap of commonly altered genes and an exclusive enrichment of overexpressed cancer genes in GBM IV. Additional analyses revealed a strong exclusive overexpression of CX3CL1 (fractalkine) and its receptor CX3CR1 in PA I possibly contributing to the absence of invasive growth. We further found that PA I was significantly associated with the mesenchymal subtype typically observed for very aggressive GBM IV. Expression of endothelial and mesenchymal markers (ANGPT2, CHI3L1) indicated a stronger contribution of the micro-environment to the manifestation of the mesenchymal subtype than the tumor biology itself. We further inferred a transcriptional regulatory network associated with specific expression differences distinguishing PA I from AS II, AS III and GBM IV. Major central transcriptional regulators were involved in brain development, cell cycle control, proliferation, apoptosis, chromatin remodeling or DNA methylation. Many of these regulators showed directly underlying DNA methylation changes in PA I or gene copy number mutations in AS II, AS III and GBM IV.ConclusionsThis computational study characterizes similarities and differences between all four astrocytoma grades confirming known and revealing novel insights into astrocytoma biology. Our findings represent a valuable resource for future computational and experimental studies.
| S-EPMC4682229 | biostudies-literature
Project description:How we perceptually organize a visual stimulus depends not only on the stimulus itself, but also on the temporal and spatial context in which the stimulus is presented and on the individual processing the stimulus and context. Earlier research found both attractive and repulsive context effects in perception: tendencies to organize visual input similarly to preceding context stimuli (i.e., hysteresis, attraction) co-exist with tendencies that repel the current percept from the organization that is most dominant in these contextual stimuli (i.e., adaptation, repulsion). These processes have been studied mostly on a group level (e.g., Schwiedrzik et al., 2014). Using a Bayesian hierarchical model comparison approach, the present study (N = 75) investigated whether consistent individual differences exist in these attractive and repulsive temporal context effects, with multistable dot lattices as stimuli. In addition, the temporal stability of these individual differences in context effects was investigated, and it was studied how the strength of these effects related to the strength of individual biases for absolute orientations. The results demonstrate that large individual differences in the size of attractive and repulsive context effects exist. Furthermore, these individual differences are highly consistent across timepoints (one to two weeks apart). Although almost everyone showed both effects in the expected direction, not every single individual did. In sum, the study reveals differences in how individuals combine previous input and experience with current input in their perception, and more generally, this teaches us that different individuals can perceive identical stimuli differently, even within a similar context.
| S-EPMC9274434 | biostudies-literature