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Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MSX1

ABSTRACT: mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 (http://r2.amc.nl) in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFβ pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.

ORGANISM(S): Homo sapiens

PROVIDER: GSE16481 | GEO | 2014/05/28

SECONDARY ACCESSION(S): PRJNA122897

REPOSITORIES: GEO

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Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MSX1

Project description:mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 (http://r2.amc.nl) in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFM-NM-2 pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival. Triplicate time course experiments of MSX1 induction, with 4 timepoints.

2014-05-28 | E-GEOD-16481 | biostudies-arrayexpress

Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MYCN

Project description:mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 (http://r2.amc.nl) in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFβ pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.

2015-10-20 | GSE16478 | GEO

Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MYCN

Project description:mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 (http://r2.amc.nl) in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFÎ² pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival. Time-course experiments in triplicate of MYCN induction after doxycycline addition, with 7 timepoints.

2015-10-20 | E-GEOD-16478 | biostudies-arrayexpress

Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma

Project description:mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFM-NM-2 pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival. 88 human Neuroblastoma samples were analyzed.

2012-03-08 | E-GEOD-16476 | biostudies-arrayexpress

Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma

Project description:mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFβ pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.

2012-03-08 | GSE16476 | GEO

Neuroblastoma cell line profiling

Project description:24 standard human Neuroblastoma Cell lines were profiled without applying any transfections in order to measure the expression profiles. Keywords: cell line, neuroblastoma, mRNA profiling. This dataset can be visualized and analyzed in the R2 platform: http://r2.amc.nl

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Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MEIS1

Project description:The pediatric tumor neuroblastoma is the second cause of cancer-related death in children. Although several recurrent gene aberrations have been found, the main signaling networks in the neuroblastoma cell, that can give important clues for more specific, more efficient treatment, is still unknown. Here we demonstrate an analysis of the MEIS1 pathway in neuroblastic tumors. It suggests important regulatory connections to tumor differentiation, cell cycle, and cell death. Time-course experiment of MEIS1-shRNA induction, with 5 timepoints.

2012-09-24 | E-GEOD-17827 | biostudies-arrayexpress

Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MEIS1

2012-09-24 | GSE17827 | GEO

Methylation of Cancer Stem Cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients

Project description:This SuperSeries is composed of the SubSeries listed below. This dataset can be analyzed and visualized in the R2 platform: http://r2.amc.nl

2011-11-05 | GSE33114 | GEO

Expression profiling of murine MYCN-driven neuroblastomas from LSL-MYCN; Dbh-iCre mice.

Project description:Amplification of MYCN is the most prominent genetic marker of high-stage neuroblastoma, a childhood tumor originating from the neural crest. We generated a transgenic mouse with Cre-conditional induction of MYCN in dopamine beta hydroxylase expressing cells that develops murine neuroblastomas. The expression profiles of six tumors from adrenals and two tumors from superial cervical gangliae were compared to three non-malignant adrenals from wildtype mice. These profiles of adrenals have been previously described (Molenaar et al., Nature Genetics 2012). Wild type samples are accessible at the AMC webpage: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi, and accessible for registered users.

2014-09-01 | E-GEOD-51297 | biostudies-arrayexpress

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