Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from human ependymoma

ABSTRACT: We compared molecular characteristics of primary and recurrent pediatric ependymoma to identify sub-group specific differences. Gene expression profiles were used to identify unique immunobiologic sub-types of posterior fossa pediatric ependymoma.

ORGANISM(S): Homo sapiens

PROVIDER: GSE50385 | GEO | 2013/08/30

SECONDARY ACCESSION(S): PRJNA217474

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from human ependymoma

Project description:We compared molecular characteristics of primary and recurrent pediatric ependymoma to identify sub-group specific differences. Gene expression profiles were used to identify unique immunobiologic sub-types of posterior fossa pediatric ependymoma. Gene expression profiles were generated from surgical tumor (ependymoma) (n=65) using Affymetrix HG-U133plus2 chips (Platform GPL570). Normalization was performed on our entire cohort of ependymoma. Of the 65 samples, a sub-set of 58 were used in the corresponding manuscript. Excluded samples are noted. Gene expression profiles were filtered to obtain gene expression of key immune cell markers. Comparative analyses between tumor samples were used to identifiy unique immunobiology between posterior fossa sub-groups.

2013-08-30 | E-GEOD-50385 | biostudies-arrayexpress

SNP microarry analysis of primary and first recurrent pediatric ependymoma

Project description:We compared genomic characteristics of primary and first recurrent pediatric ependymoma to identify sub-group specific differences.

2016-09-11 | GSE50876 | GEO

Whole-genome microRNA microarray for CD44 positive and negative pediatric posterior fossa ependymoma

Project description:we used whole-genome microRNA microarray expression profiling as a discovery platform to identify a subset of miRNAs that were differently expressed in CD44-positive pediatric posterior fossa ependymoma compared with CD44-negative ones.

2021-03-20 | GSE112103 | GEO

Ependymoma subpopulation lineages underlie clinical classification and outcome (microarray data set)

Project description:Introduction: single-cell RNA sequencing identified multiple subpopulations in childhood posterior fossa ependymoma. The contribution of individual neoplastic subpopulations to bulk tumor transcriptome-based molecular classification and patient outcome was estimated by deconvolution in a cohort of clinically-annotated primary and recurrent EPN samples. The abundance of EPN subpopulations was estimated in primary EPN samples and showed that the ratio of subpopulation fractions dictated assignment to the two main transcriptomic classification subgroups in childhood posterior fossa ependymoma. Longitudinal analysis revealed that subpopulation fractions changed between presentation and recurrence. Outcome analyses demonstrated that a different proportions of subpopulations were associated with differential survival.

2020-07-31 | GSE125861 | GEO

RNA sequencing of posterior fossa ependymoma harboring 6q loss

Project description:Two distinct groups of posterior fossa ependymoma, PF-EPN-A and PF-EPN-B have been identified in children and are often associated with widely distinct outcomes. We have identified an ultra-high-risk PF-EPN-A ependymoma with 6q loss. We performed RNA sequencing of posterior fossa ependymoma A (PF-EPN-A) tumor samples with chromosome 6q loss and balanced to understand the differences in 6q loss at the transcriptomic level

2021-02-15 | GSE164292 | GEO

ACVR1-mutant posterior fossa ependymoma

Project description:ACVR1-mutant posterior fossa ependymoma

| PRJNA802906 | ENA

Pro-Inflammatory Cytokines Mediate the Epithelial-to-Mesenchymal-Like Transition of Pediatric Posterior Fossa Ependymoma (single-nucleus ATAC-seq)

Project description:Pediatric ependymoma is a devastating brain cancer marked by its relapsing pattern and lack of effective chemotherapies. This shortage of treatments is due to limited knowledge about ependymoma tumorigenic mechanisms. By means of single-nucleus chromatin accessibility and gene expression profiling of posterior fossa primary tumors and distal metastases, we reveal key transcription factors and enhancers associated with the differentiation of ependymoma tumor cells into tumor-derived cell lineages and their transition into a mesenchymal-like state. We identify NFkB, AP-1, and MYC as mediators of this transition, and show that the gene expression profiles of tumor cells and infiltrating microglia are consistent with abundant pro-inflammatory signaling between these populations. In line with these results, both TGF-b1 and TNF-a induce the expression of mesenchymal genes on a patient-derived cell model, and TGF-b1 leads to an invasive phenotype. Altogether, these data suggest that tumor gliosis induced by inflammatory cytokines and oxidative stress underlies the mesenchymal phenotype of posterior fossa ependymoma.

2022-06-24 | GSE206579 | GEO

Pro-Inflammatory Cytokines Mediate the Epithelial-to-Mesenchymal-Like Transition of Pediatric Posterior Fossa Ependymoma (single-nucleus RNA-seq)

2022-06-24 | GSE206578 | GEO

Pro-Inflammatory Cytokines Mediate the Epithelial-to-Mesenchymal-Like Transition of Pediatric Posterior Fossa Ependymoma

2022-06-24 | GSE206580 | GEO

Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

Project description:Gene expression (mRNA) profiling of human ependymomas Despite the histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymoma. Group-A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, secondary metastasis, and death as compared to Group-B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third independent group of tumors using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients. We analyzed 102 primary ependymomas on the Affymetrix Exon 1.0ST platform (Gene Level).

2011-08-14 | E-GEOD-27279 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data