Figure S1. Nestin mRNA is differentially expressed in brain tumors and normal brain tissue. The database R2 was searched for nestin expression using publicly available datasets. Nestin is highly expressed in ependymoma (red) and astrocytomas and gliomas (astrocytoma, oligodendroglioma, anaplastic astrocytoma, anaplastic oligoastrocytoma, glioblastoma; blue), but not in medulloblastomas (blue). Normal adult tissue of varying brain regions (green) show low expression, while embryonal tissue shows high expression of nestin (green). Numbers following an underscore indicate the total numbers of samples in each dataset; in the second ependymoma dataset, letters following “83:” indicate the molecular subgroup; in the medulloblastoma, dataset letters following “120:” indicate the subgroup; in the embryogenesis, dataset numbers following “18:” indicate the week of human embryonic development; lca = large cell anaplastic; nd = not determined.

Figure S2. Nestin protein is differentially expressed in ependymoma of differing location and grade. While no differences in nestin-positive and -negative ependymoma were found regarding gender or resection status, a significantly higher proportion of nestin-positive ependymoma was found in all supratentorial and WHO III ependymoma. When separated by age groups, a significantly higher proportion of pediatric supratentorial, and adult WHO III ependymoma were found to be nestin positive. infra = infratentorial; supra = supratentorial; STR = subtotal resection; GTR = gross total resection; nes = nestin; pos = positive; neg = negative; n.s. = not significant; *P < 0.05, **P < 0.005, ***P < 0.0001 (Fisher&apos;s exact t-test).

Table S1. Cox proportional hazards model for progression-free (PFS) and overall survival (OS) estimation—univariable analysis. HR = hazard ration; CI = confidence interval.

Table S2. Five-year progression-free (PFS) and overall survival (OS). infra = infratentorial; supra = supratentorial; neg = negative; pos = positive; infra = infratentorial; supra = supratentorial; PFA = posterior fossa group A; PFB = posterior fossa group B.

Table S3. Genes co-regulated (correlation coefficient >0.5) with nestin from the Heidelberg dataset, ranked by correlation coefficient.

Table S4. Genes significantly co-regulated (correlation coefficient >0.5) with nestin from the Toronto dataset, ranked by correlation coefficient.

Table S5. Genes co-regulated with nestin found in both datasets (Heidelberg and Toronto), ranked by correlation coefficient for each dataset and displayed according to average rank.

Table S6. Gene sets in the Heidelberg or Toronto dataset with significant adjusted P-value in both hypergeometric test and gene set enrichtment analysis (GSEA), with genes from the respective dataset (Supporting Table S3 or S4) in alphabetical order.

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