Project description:Interventions: Group 1: Quantitative Expression Analysis of the proteom and gene Expression of Primary Tumor, normal tissue, and metastases
Primary outcome(s): Disease associated Proteins and Genes
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: basic science
Project description:Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, a dozen reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. For most organisms, however, few or no such reference datasets are publicly available. Here, we describe a new type of datasets highly representative for the spatial, temporal and response dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments and aggregating results by anatomical parts, stages of development, perturbations, drugs, diseases, neoplasms, and genotypes. The proposed datasets were created for human and several model organisms and are publicly available at www.expressiondata.org.
Project description:Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, a dozen reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. For most organisms, however, few or no such reference datasets are publicly available. Here, we describe a new type of datasets highly representative for the spatial, temporal and response dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments and aggregating results by anatomical parts, stages of development, perturbations, drugs, diseases, neoplasms, and genotypes. The proposed datasets were created for human and several model organisms and are publicly available at www.expressiondata.org. PMI: 18 Samples were used with 2 different experimental factors: 1. 2 harvesting times (morning/afternoon) 2. 3 pos-harvesting times. 3 biological replicates were used.
Project description:RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors understand how patients respond to treatment.
PURPOSE: This laboratory study is looking at gene expression in patients with advanced or metastatic colorectal cancer receiving bevacizumab.
Project description:1.1 To collect pathological tumor specimens of patients with metastatic colorectal cancer in a prospective fashion for correlative studies of response to an oxaliplatin based chemotherapy regimen.
1.2 To determine a gene expression profile that predicts response to an oxaliplatin based chemotherapy regimen in this cohort of patients.
Project description:Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes
