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17 APR 2008
NEW STUDIES ADD CANCER PATHWAYS, DNA AMPLIFICATIONS, DRUG SENSITIVITY, AND ADDITIONAL CANCER SIGNATURES FOR TARGET DISCOVERY AND BIOMARKER ANALYSIS

As the Oncomine collection of cancer profiling data grows, Compendia Bioscience continually looks for data that can help to unravel the complexity of cancer biology. In this release we focus on cancer pathway data, while also expanding the expO dataset and adding new ChIP-on-chip literature defined concepts.

  • New Pathway Datasets – Highly curated data from 19 additional studies, focusing on Notch, PTEN, EGF, and EZH2, are now available. more->

  • Updated expO Dataset – The Bittner_Multi-cancer dataset has been re-loaded with new data on over 1,900 samples, covering 39 different cancer subtypes. more->

  • Paired aCGH/mRNA Datasets – There are now five pairs of studies with gene expression and amplification data on the sample samples. morex

  • Additional Concepts – New literature-defined concepts have been included, featuring ChIP-on-chip technology, shRNA findings, and the IGF pathway. All new differential expression analyses create additional Oncomine concepts as well. more->

  • Data Changes – As part of Compendia’s commitment to improving the curation and annotation of our data, changes may be made to previously released Oncomine datasets. These changes can include additional differential expression analyses and heatmap grouping options, as well as modified profile wording and analysis removal. All changes to Oncomine content are documented; a list of all changes is available upon request.  Major changes can be found Here ->.

In addition to these highlights, this data release includes further drug treatment studies, a new large cell line panel (Wagner_CellLine, n=119) dataset, and additional differential expression analyses on Burkitt Lymphoma vs. DLBCL.

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What it means

Array CGH studies provide additional information to supplement mRNA expression data on the copy number of genes at the DNA level. Comparing copy number data to gene expression data can be useful in identifying and validating the potential genes involved in cancer. In Oncomine, aCGH studies are handled similarly to gene expression studies. If a significant result is observed in Diff/Ex, Co/Ex or Outlier analyses, the data will be presented alongside gene expression data. Note that now each result is marked with experiment type, differentiating mRNA from aCGH data. Also, aCGH studies can be specifically found by Filtering on Experiment Type>DNA in both the gene and profile modules under the Diff/Ex, Co/Ex and Outlier tabs.
 
 
Inferring Actual Copy Number
To interpret aCGH analysis in Oncomine, view the Log2 scale considering zero as a "normal state" where an individual has two copies of a gene. Thus, a unit of 1 on the y-axis is interpreted as 2-fold more copies (or 4 copies) and a unit of -1 is interpreted as 0.5-fold copies (or 1 copy). This requires one to assume the median copy number (zero) is 2 copies.

Did you know
Our support staff is continually working on new materials for users. A Flash demo and quickstart guide on using pathway activation signatures is available for registered users. morex

About Compendia Bioscience, Inc.
Compendia Bioscience is dedicated to harnessing the global collection of high throughput molecular data to provide researchers with the data and analysis tools necessary to validate biomarker and gene target discoveries, better understand mechanisms of disease, and optimize clinical outcomes.

 
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