Transcriptomics,Multiomics

Dataset Information

42

DNA methylation data from pilocytic astrocytoma tumor samples and normal cerebellum controls


ABSTRACT: Pilocytic astrocytomas (PA) are the most common brain tumor in pediatric patients and can cause significant morbidity, including chronic neurological deficiencies. They are characterized by activating alterations in the mitogen-activated protein kinase (MAPK) pathway, but little else is known about their development. To map the global DNA methylation profiles of these tumors, we analysed 61 PAs and 6 normal cerebellum samples using Illumina's Infinium HumanMethylation450 BeadChips. These data revealed two subgroups of PA that separate according to tumor location (infratentorial versus supratentorial), and identified key neural developmental genes that are differentially methylated between the two groups. Integration with transcriptome microarray data highlighted significant expression differences, which were unexpectedly associated with a strong positive correlation between methylation and expression. Differentially methylated probes were often identified within the gene body and/or regions up- or downstream of the gene, rather than at the transcription start site. We also identified a large number of differentially methylated genes between cerebellar PAs and normal cerebellum, which included additional developmental genes. Bisulphite converted DNA from 61 PA tumours (fresh frozen) and 6 normal cerebellum (from commerical sources) were hybridised to the Illumina Infinium HumanMethylation450 BeadChips.

OTHER RELATED OMICS DATASETS IN: PRJNA190897PRJNA192667

ORGANISM(S): Homo Sapiens

TISSUE(S): Pilocytic Astrocytoma Tumor, Normal Cerebellum

SUBMITTER: Hendrik Witt   Marina Ryzhova  Volker Hovestadt  Peter Lichter  Marcel Kool  Manuela Zucknick  Danita M Pearson  David T Jones  Sally R Lambert  Adam Fontebasso  V P Collins  Nada Jabado  Stefan M Pfister  Koichi Ichimura  Andrey Korshunov 

PROVIDER: E-GEOD-44684 | ArrayExpress | 2013-06-12

SECONDARY ACCESSION(S): GSE44684PRJNA190897

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-44684.additional.1.zip Other
E-GEOD-44684.additional.2.zip Other
E-GEOD-44684.idf.txt Idf
E-GEOD-44684.processed.1.zip Processed
E-GEOD-44684.processed.2.zip Processed
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Publications

Differential expression and methylation of brain developmental genes define location-specific subsets of pilocytic astrocytoma.

Lambert Sally R SR   Witt Hendrik H   Hovestadt Volker V   Zucknick Manuela M   Kool Marcel M   Pearson Danita M DM   Korshunov Andrey A   Ryzhova Marina M   Ichimura Koichi K   Jabado Nada N   Fontebasso Adam M AM   Lichter Peter P   Pfister Stefan M SM   Collins V Peter VP   Jones David T W DT  

Acta neuropathologica 20130510 2


Pilocytic astrocytomas (PAs) are the most common brain tumors in pediatric patients and can cause significant morbidity, including chronic neurological deficiencies. They are characterized by activating alterations in the mitogen-activated protein kinase pathway, but little else is known about their development. To map the global DNA methylation profiles of these tumors, we analyzed 62 PAs and 7 normal cerebellum samples using Illumina 450K microarrays. These data revealed two subgroups of PA th  ...[more]

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