Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human neuroblastoma cell lines grown under normoxic and hypoxic conditions

ABSTRACT: Hypoxia is a low oxygen condition that occurs in the developing tumor mass and that is associated with poor prognosis and resistance to chemo- and radio-therapy. The definition of the hypoxia gene signature is fundamental for the understanding of tumor biology, as in the case of neuroblastoma, the most common pediatric solid tumor. The issue of identifying a significant group of variables in microarray gene expression experiments is particularly difficult due to the typical high dimensional nature of the data and great effort has been spent in the development of feature selection techniques. Our main goal is to define a robust hypoxia gene signature in neuroblastoma cell lines. A set of 11 neuroblastoma cell lines were cultured under normoxic and hypoxic conditions for 18 hours, and their gene expression profiles were measured with Affymetrix GeneChip HG-U133 Plus 2.0. We used the l1-l2 regularization framework in order to select the significant probesets defining hypoxic versus normoxic cell lines. Experiment Overall Design: The expression profiles of 11 neuroblastoma cell lines under normoxia vs hypoxia were studied.

ORGANISM(S): Homo sapiens

SUBMITTER: Paolo Fardin

PROVIDER: E-GEOD-17714 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A biology-driven approach identifies the hypoxia gene signature as a predictor of the outcome of neuroblastoma patients.

Fardin Paolo P Barla Annalisa A Mosci Sofia S Rosasco Lorenzo L Verri Alessandro A Versteeg Rogier R Caron Huib N HN Molenaar Jan J JJ Ora Ingrid I Eva Alessandra A Puppo Maura M Varesio Luigi L

Molecular cancer 20100712

<h4>Background</h4>Hypoxia is a condition of low oxygen tension occurring in the tumor microenvironment and it is related to poor prognosis in human cancer. To examine the relationship between hypoxia and neuroblastoma, we generated and tested an in vitro derived hypoxia gene signature for its ability to predict patients' outcome.<h4>Results</h4>We obtained the gene expression profile of 11 hypoxic neuroblastoma cell lines and we derived a robust 62 probesets signature (NB-hypo) taking advantage ...[more]

PMID: 20624283

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Dataset Information

Transcription profiling of human neuroblastoma cell lines grown under normoxic and hypoxic conditions

Publications

A biology-driven approach identifies the hypoxia gene signature as a predictor of the outcome of neuroblastoma patients.

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