Oncomine Data Newsletter

 

01 OCT 2009
Oncomine: 500 Strong and Still Growing

The Compendia data team is proud to announce the addition of 22 new studies, bringing our total study count to 501. As always, we’ve added a range of Sensitivity, Treatment, Transfection, and Mutation data, as well as large Tumor datasets and Cell Line Panels.

Highlights

-> VIEW ALL NEW STUDIES  

In addition to these new studies, existing studies have been improved, Oncomine clusters refined, and duplicate datasets removed. For more details, view the Data Release notes available under Help in the application. -> GO TO ONCOMINE 4.2

Additional changes to previously released Oncomine datasets may be made as we continually improve the curation and annotation of our data. Changes to content are documented and major changes can be found -> HERE (PDF).

tips & tricks

NEW EXPRESSION DATA ISN'T THE ONLY BIG NEWS.

The data team has also been working to expose additional sample data from existing studies in the same clear, standardized format that has become the hallmark of the Compendia Ontology:

New! Triple Negative Status
The new Triple Negative Filter identifies cancer samples that are negative for the ERBB2, ER, and PR markers. To find this data, type Triple in the search box, then select either Molecular Subtype (to find all datasets that include samples with Triple Negative Status) or Analysis Type (to find analyses that compare Triple Negative samples with samples of other biomarker statuses).
tripple negative

New! Demographics Data
The new Demographics Filter provides an entry point for identifying datasets with demographic data such as age, race/ethnicity, sex, or smoking status:
demographics

New! Epi vs. Stroma Analyses
Earlier this year we introduced new Tissue Subtype terminology to describe tumor samples that contain purified Epithelia or purified Stroma; since then, analyses that include those samples have been restricted to one subtype or the other. With this release we’ve added a new analysis that compares Epithelia and Stroma to each other. These analyses can be found in the Analysis Type part of the Filter Tree, under Cancer Subtype Analysis, and provide a nice way to determine quickly which genes in a pathway of interest are expressed in the stroma, and which in the epithelia, as shown here for the Wnt pathway in Ovarian tissues:

Click for bigger view
analysis
 
Spotlight

Experimental Interplay between Cell Line and Tumor Data

It's no accident that the Compendia data team conspires to build a strong foundation of both cell line and tumor data: in Oncomine, the co-existence of these two data types makes otherwise difficult inquiries possible.

For example, a great strength of cell line data is the ability to generate tightly controlled experimental results, in which only one thing varies between experimental and control samples. One of our favorites is the over-expression of a single oncogene (RAS) in a normal cell line (HMEC) to determine the set of genes affected by that oncogene (Bild CellLine).

In Oncomine, this interesting result becomes a powerful new tool that can be used to assay any or all of the 34,500+ existing tumor samples in Oncomine for groups of samples in Oncomine Concepts — or for individual samples using the Export function — that similarly mis-express the gene set of interest.

Thus every time we add a new cell line experiment with a clear functional signature, we provide a new opportunity to query the 34,500+ tumor samples for that signature — and every time we add new tumor data, we provide the reverse: a new opportunity to re-analyze existing cell line signatures against new tumor data.

We like to think that by focusing on both cell line and tumor data, we provide not just more data with each new study, but also more experimental opportunity.

Happy hunting.


CONTACT: Compendia Bioscience