Kenya_HM3_imputed - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010000570 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Imputation-based meta-analysis of severe malaria in Gambia.
| EGAD00010000572 | EGA
Project description:Genome-wide study of resistance to severe malaria in eleven worldwide populations:Kenya
| EGAD00010000904 | EGA
Project description:EGAS00001001311: Genome-wide study of resistance to severe malaria in eleven worldwide populations:Kenya
| EGAD00010001742 | EGA
Project description:DCEG Imputation Reference Dataset
| PRJNA75845 | ENA
Project description:Host factors governing mild disease in adults who have developed clinical immunity to Plasmodium falciparum may provide insights for disease altering vaccine or interventions, to prevent severe malaria We used microarrays of whole blood samples during mild malaria and compared them in a paired analysis to whole blood microarray 30 days later. (n=19 pairs)
2014-12-19 | GSE64338 | GEO
Project description:Abstract of associated publication: Background: During the latter half of the natural 48-hour intraerythrocytic life cycle of human Plasmodium falciparum infection, parasites sequester deep in endothelium tissues, away from the spleen and inaccessible to peripheral blood. These late-stage parasites may cause tissue damage and likely contribute to clinical disease, and a more complete understanding of their biology is needed. Because these life cycle stages are not easily sampled due to deep tissue sequestration, measuring in vivo gene expression of parasites in the trophozoite and schizont stages has been a challenge. Methods: We developed a custom nCounter® gene expression platform, and used this platform to measure malaria parasite gene expression profiles in vitro and in vivo. We also used imputation to generate global transcriptional profiles, and assessed differential gene expression between parasites growing in vitro and those recovered from malaria-infected patient tissues collected at autopsy. Results: We demonstrate, for the first time, global transcriptional expression profiles from in vivo malaria parasites sequestered in human tissues. We found that parasite physiology can be correlated with in vitro data from an existing life cycle data set, and that parasites in sequestered tissues show an expected schizont-like transcriptional profile, which is conserved across tissues from the same patient. Imputation based on 60 landmark genes generated global transcriptional profiles that were highly correlated with genome-wide expression patterns from the same sample measured by microarray. Finally, differential expression revealed a limited set of in vivo upregulated transcripts, which may indicate unique parasite genes involved in human clinical infections. Conclusions: Our study highlights the utility of a custom nCounter® P. falciparum probe set, validation of imputation within Plasmodium species, and documentation of in vivo schizont-stage expression patterns from human tissues.
2014-11-15 | GSE63260 | GEO
Project description:Severe thrombocytopenia can be a determinant factor in the morbidity of Plasmodium vivax (Pv), the most widespread human malaria. Although immune mechanisms may drive Pv-induced severe thrombocytopenia (PvST), the current data on the cytokine landscape in PvST is scarce, and often conflicting. The analysis of the bidirectional circuit of inflammatory mediators and miRNAs would lead to a better understanding of the mechanisms underlying PvST.
2021-03-15 | GSE162304 | GEO
Project description:<p>The malaria parasite life cycle includes asexual replication in human blood, with a proportion of parasites differentiating to gametocytes required for transmission to mosquitoes. Commitment to differentiate into gametocytes, which is marked by activation of the parasite transcription factor <em>ap2-g</em> , is known to be influenced by host factors but a comprehensive model remains uncertain. Here we analyze data from 828 children in Kilifi, Kenya with severe, uncomplicated, and asymptomatic malaria infection over 18 years of falling malaria transmission. We examine markers of host immunity and metabolism, and markers of parasite growth and transmission investment. We find that inflammatory responses and reduced plasma lysophosphatidylcholine levels are associated with markers of increased investment in parasite sexual reproduction (i.e., transmission investment) and reduced growth (i.e., asexual replication). This association becomes stronger with falling transmission and suggests that parasites can rapidly respond to the within-host environment, which in turn is subject to changing transmission.</p>
2025-07-09 | MTBLS5130 | MetaboLights
Project description:Major depressive disorder is a heterogeneous illness with a mostly uncharacterized pathology. Large scale gene expression (transcriptome) analysis and genome-wide association studies (GWAS) for single nucleotide polymorphisms have generated a considerable amount of gene- and disease-related information, but heterogeneity and various sources of noise have limited the discovery of disease mechanisms. As systematic dataset integration is becoming essential, we developed methods and performed meta-clustering of gene coexpression links in 11 transcriptome studies from postmortem brains of human subjects with major depressive disorder (MDD) and non-psychiatric control subjects. We next sought enrichment in the top 50 meta-analyzed coexpression modules for genes otherwise identified by GWAS for various sets of disorders. One coexpression module of 88 genes was consistently and significantly associated with GWAS for MDD, other neuropsychiatric disorders and brain functions, and for medical illnesses with elevated clinical risk of depression, but not for other diseases (See publication for details).
2014-05-16 | GSE54566 | GEO