60+ New Datasets, Standardized Sample Terminology, and Enhanced Concept Organization

For this data release, the Compendia Bioscience team has worked to bring you 62 new, highly curated datasets. A few highlighted datasets are below (the complete list can be found by clicking on the more link).

• Wooster CellLine 2 — Affymetrix 500K SNP profiling of GlaxoSmithKline’s 300+ cell line panel
• Weir Lung — Affymetrix 250K SNP profiling of 371 lung adenocarcinoma samples
• TCGA Brain and TCGA Ovarian — glioblastoma and ovarian serous cystadenocarcinoma samples from the Cancer Genome Atlas
• Mulligan Myeloma — 264 multiple myeloma samples with Bortezomib or Dexamethasone response data
• Sorich Leukemia — 161 childhood acute lymphoblastic leukemia samples with Methotrexate response data
• Raponi Leukemia — 34 acute myeloid leukemia samples with Tipifarnib response data
• Ding Lung — 75 lung carcinoma samples with mutation data on 76 different genes
• Shankavaram CellLine 2 — NCI-60 cell line panel profiled on Affymetrix U95A microarrays
  MORE

Compendia Ontology
In conjunction with the release of Oncomine 4.0, the sample terminology for every dataset in Oncomine was revisited. We have now applied a controlled vocabulary (the Compendia Ontology) that unifies the samples with consistent, understandable annotations. This controlled vocabulary complements changes in the application, such that samples and analyses with similar properties are easily identified across the database. Normalized terminology is now used for diseases, clinical outcomes, molecular aberrations, treatments, transfections, and cell line names, and all of these terms are now easily searchable and browse-able through Oncomine 4.0. In addition, we’ve leveraged the Compendia Ontology to create new, standardized differential expression analyses that return more consistent results.

Concepts. Organized.
We have also enhanced the organization of all concepts in Oncomine 4.0. Concepts have been grouped into high-level categories: Biology Concepts (including biological annotations, pathway concepts, and regulatory concepts), Mutation Concepts (including CAN Genes, COSMIC, and Cancer Gene Census), Oncomine Clusters, Oncomine Gene Expression Signatures, shRNA Concepts, literature-defined concepts, and Connectivity Map Drug Signatures. In addition to the multi-layered concept organization, the Connectivity Map Drug Signatures have also been updated to the latest version (build 02).