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Home › Dataset Library › Gene expression data from pilocytic astrocytoma tumour samples and normal cerebellum controls

Dataset: Gene expression data from pilocytic astrocytoma tumour samples and normal cerebellum controls

Pilocytic astrocytomas (PA) are the most common brain tumor in pediatric patients and can cause significant morbidity, including chronic...

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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 further define their molecular development, we analysed the global DNA methylation profiles of 61 PAs and 6 normal cerebellum samples and integrated this data with transcriptome profiling. 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. Significant expression differences were identified for the majority of differentially methylated genes, and these were unexpectedly associated with a strong positive correlation between methylation and expression. We also identified a large number of differentially methylated/expressed genes between cerebellar PAs and normal cerebellum, which included additional developmental genes. Total RNA from 49 PA tumour samples and 9 normal cerebellum samples (from commercial sources) were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays.

Species:
human

Samples:
58

Source:
E-GEOD-44971

PubMed:
23660940

Updated:
Dec.12, 2014

Registered:
Jul.12, 2014


Factors: (via ArrayExpress)
Sample ORGANISM PART MAPK HIT AGE AT DIAGNOSIS YEARS DNA METHYLATION SUBGROUP SEX BRAIN LOCATION
GSM109487 Normal cerebellum control Pilocytic astrocytoma: N/A 26 N/A male cerebellum
GSM1094870 Normal cerebellum control Pilocytic astrocytoma: N/A adult N/A male cerebellum
GSM1094870 Normal cerebellum control Pilocytic astrocytoma: N/A adult N/A male cerebellum
GSM1094868 Normal cerebellum control Pilocytic astrocytoma: N/A 24 N/A male cerebellum
GSM1094867 Normal cerebellum control Pilocytic astrocytoma: N/A Fetal N/A female cerebellum
GSM1094866 Normal cerebellum control Pilocytic astrocytoma: N/A Fetal N/A male cerebellum
GSM1094866 Normal cerebellum control Pilocytic astrocytoma: N/A Fetal N/A male cerebellum
GSM1094867 Normal cerebellum control Pilocytic astrocytoma: N/A Fetal N/A female cerebellum
GSM1094867 Normal cerebellum control Pilocytic astrocytoma: N/A Fetal N/A female cerebellum
GSM1094862 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 12 1 male diencephalon
GSM109486 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 8 2 female cerebellum
GSM1094860 Pilocytic Astrocytoma Pilocytic astrocytoma: BRAF V600E 3 1 female optic nerve
GSM1094859 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 3 2 male cerebellum
GSM1094858 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9 26 NA female cerebellum
GSM1094857 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 9 2 female cerebellum
GSM1094856 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 11 2 female cerebellum
GSM1094855 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 3 2 female cerebellum
GSM1094854 Pilocytic Astrocytoma Pilocytic astrocytoma: NF1 12 NA female Left frontal lobe
GSM1094853 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 16 NA male cerebellum
GSM1094852 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 20 NA female cerebellum
GSM109485 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 4 2 male cerebellum
GSM1094850 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 26 NA female cerebellum
GSM1094849 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:11 25 NA male cerebellum
GSM1094848 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 9 1 male Fourth Ventricle
GSM1094847 Pilocytic Astrocytoma Pilocytic astrocytoma: None identified 14 2 female cerebellum
GSM1094852 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 20 NA female cerebellum
GSM1094845 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 6 2 female cerebellum
GSM109485 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 4 2 male cerebellum
GSM1094843 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9 8 1 female cerebral hemisphere
GSM1094842 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9 7 1 male Brainstem
GSM109484 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 5 2 male cerebellum
GSM1094840 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 6 2 male cerebellum
GSM109485 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 4 2 male cerebellum
GSM1094838 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 2 2 male cerebellum
GSM1094837 Pilocytic Astrocytoma Pilocytic astrocytoma: BRAF V600E 3 1 female diencephalon
GSM1094836 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 10 2 male cerebellum
GSM1094835 Pilocytic Astrocytoma Pilocytic astrocytoma: KRAS E63K 11 2 female cerebellum
GSM1094834 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 22 2 female cerebellum
GSM1094833 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 12 1 female diencephalon
GSM1094832 Pilocytic Astrocytoma Pilocytic astrocytoma: BRAF ins598T 17 2 female cerebellum
GSM109483 Pilocytic Astrocytoma Pilocytic astrocytoma: NF1; KIAA1549:BRAF fusion_15:9; BRAF V600E 3 1 female diencephalon
GSM1094830 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:11 11 2 male cerebellum
GSM1094829 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9 19 2 male cerebellum
GSM1094828 Pilocytic Astrocytoma Pilocytic astrocytoma: NF1; KIAA1549:BRAF fusion_breakpoint not determined 3 1 male diencephalon
GSM1094827 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 13 2 male cerebellum
GSM1094826 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9 10 2 male cerebellum
GSM1094825 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_breakpoint not determined 2 1 female diencephalon
GSM1094824 Pilocytic Astrocytoma Pilocytic astrocytoma: BRAF V600E 14 1 male cerebral hemisphere
GSM1094823 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 16 2 male cerebellum
GSM109485 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 4 2 male cerebellum
GSM109482 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9 11 2 female cerebellum
GSM1094820 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9 2 2 male cerebellum
GSM1094819 Pilocytic Astrocytoma Pilocytic astrocytoma: FAM131B:BRAF fusion 16 1 male cerebral hemisphere
GSM1094818 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 5 2 female cerebellum
GSM1094817 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 4 2 female cerebellum
GSM1094816 Pilocytic Astrocytoma Pilocytic astrocytoma: None identified 17 NA male cerebral hemisphere
GSM1094815 Pilocytic Astrocytoma Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9 9 2 male cerebellum
GSM1094814 Pilocytic Astrocytoma Pilocytic astrocytoma: None identified 21 NA male cerebellum

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  • brain
  • cerebellum
  • protein

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