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Transcription profiling of human ependymoma tumors with known clinical outcomes

ABSTRACT: Ependymoma, the 3rd most common brain tumor in children, recurs in approximately 50% of patients. There is currently no robust marker that predicts for recurrence, which is a significant clinical problem; We used global gene expression profiling of 19 patient surgical samples obtained at initial diagnosis and with known clinical outcomes to discover novel prognostic markers. Experiment Overall Design: Gene expression profiles were generated from surgical tumor samples using Affymetrix HG-U133plus2 chips. Profiles were divided into recurrent and non-recurrent groups in order to identify differentially expressed genes that were associated with risk of recurrence. In addition, time to progression was correlated with gene expression as a continuous variable in the recurrent group.

ORGANISM(S): Homo sapiens

SUBMITTER: Donson Andrew

PROVIDER: S-ECPF-GEOD-16155 | biostudies-other |

REPOSITORIES: biostudies-other

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Transcription profiling of human ependymoma tumors with known clinical outcomes

Project description:Ependymoma, the 3rd most common brain tumor in children, recurs in approximately 50% of patients. There is currently no robust marker that predicts for recurrence, which is a significant clinical problem; We used global gene expression profiling of 19 patient surgical samples obtained at initial diagnosis and with known clinical outcomes to discover novel prognostic markers. Experiment Overall Design: Gene expression profiles were generated from surgical tumor samples using Affymetrix HG-U133plus2 chips. Profiles were divided into recurrent and non-recurrent groups in order to identify differentially expressed genes that were associated with risk of recurrence. In addition, time to progression was correlated with gene expression as a continuous variable in the recurrent group.

2009-10-10 | E-GEOD-16155 | biostudies-arrayexpress

Transcription profiling of primary human breast tumors showing poor clinical prognosis

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Transcription profiling of human glial brain tumors

Project description:Gene expression profiling in 50 glial brain tumors and 4 normal brains using 42,000-feature cDNA microarrays (from total RNA). Tumors: 50 fresh-frozen glioma specimens subjected to standard WHO classification. Specimens included astrocytic [2 juvenile pilocytic astrocytomas, 1 low-grade astrocytic glioma, 1 anaplastic astrocytomas, 31 glioblastomas (of these 2 secondary glioblastomas and 2 gliosarcomas)], oligodendroglial [5 oligodendrogliomas, 3 anaplastic oligodendrogliomas], and 6 anaplastic oligoastrocytomas tumors. One tumor had been classified as glioneuronal neoplasm. Normal brain was purchased from Stratagene. Stratagene Universal Common Reference was used as reference RNA. The results provide insights into molecular mechanisms and pathways associated with gliomagenesis.

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Transcription profiling by array of human pancreatic tumors

Project description:We used microarrays to identify the expression differences of FKBP5 gene between the pancreatic tumor and normal samples. On average normal samples had more FKBP5 expression compared to tumor samples .Experiment Overall Design: This experiment consists of 36 tumor samples and 16 normal samples; a total of 52 samples. 16 samples consist of both tumor and normal expression data, whereas 20 samples consist of only tumor data.

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Transcription profiling of human age-dichotomized ER+ breast tumors

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Optimized ChIP-seq method facilitates transcription factor profiling in human tumors.

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Transcription profiling of human breast tissue tumors vs. normal tissue

Project description:bulk breast tumor RNA from patient; Abstract: Sporadic basal-like cancers (BLC) are a distinct class of human breast cancers that are phenotypically similar to BRCA1-associated cancers. Like BRCA1-deficient tumors, most BLC lack markers of a normal inactive X chromosome (Xi). Duplication of the active X chromosome and loss of Xi characterized almost half of BLC cases tested. Others contained biparental but nonheterochromatinized X chromosomes or gains of X chromosomal DNA. These abnormalities did not lead to a global increase in X chromosome transcription but were associated with overexpression of a small subset of X chromosomal genes. Other, equally aneuploid, but non-BLC rarely displayed these X chromosome abnormalities. These results suggest that X chromosome abnormalities contribute to the pathogenesis of BLC, both inherited and sporadic. total 62 sample incudes 43 tumor, 7 normal breast and 12 normal organelle Experiment Overall Design: compare expression of tumor to normal breast tissue

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Transcription profiling of 67 human lung tumors representing 56 patients

Project description:The global gene expression profiles for 67 human lung tumors representing 56 patients were examined by using 24,000-element cDNA microarrays. Subdivision of the tumors based on gene expression patterns faithfully recapitulated morphological classification of the tumors into squamous, large cell, small cell, and adenocarcinoma. The gene expression patterns made possible the subclassification of adenocarcinoma into subgroups that correlated with the degree of tumor differentiation as well as patient survival. Gene expression analysis thus promises to extend and refine standard pathologic analysis.

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microRNA profiling and clinical outcomes in human osteosarcoma (biopsies)

Project description:Osteosarcoma is a malignancy with variable outcomes that are not tightly aligned with chemotherapy response. Previous work has suggested a possible role for microRNAs (miRNAs) in determining the susceptibility of osteosarcomas to treatment but formal miRNA-based outcome models have not been reported. Formalin-fixed, paraffin-embedded (FFPE) specimens may be a unique approach for such studies in a rare malignancy. We used supervised principal components analysis and logistic regression to study survival and chemoresponse endpoints, and miRNA activity and gene set analysis algorithms to study miRNA regulatory networks using mRNA data. Our study also creates a paradigm for FFPE-based miRNA clinical biomarker research in rare tumors.

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mRNA profiling and clinical outcomes in human osteosarcoma (biopsies)

2013-01-22 | GSE39055 | GEO