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Category Genomics>Gene Expression Analysis/Profiling/Tools Abstract Oncomine Concepts Map (OCM) is a web-based resource that researchers can access as an additional component of Oncomine Professional (see G6G Product Number 20014). OCM has the ability to leverage publicly available high-throughput molecular profiling data to produce something new - biological insight into the genetic associations that link over 18,000 individual gene, protein, drug, and pathways signatures from the literature and other public and private sources. OCM uses experimentally defined gene sets as a common language for the systematic comparison of biological concepts from heterogeneous sources, so that when distinct biological phenomena share similar sets of gene expression patterns, those linkages can be detected. Product features/benefits include:
as a set of genes (a gene “signature”) that is characteristically associated with some biological phenomena (e.g., differential expression in disease or after drug treatment, or genes involved in a specific pathway or regulatory mechanism). To date, over 18,000 biologically related sets of genes have been defined from over 18,000 microarray experiments and 12 sources of reference data. These are the types of molecular concepts used in OCM. Oncomine Professional - Cancer signatures used in OCM are derived from 1,100+ Oncomine analyses that compare gene expression patterns between logical groupings of normal and malignant human tissues or cell-lines. Oncomine (database) currently contains cancer- relevant data from over 18,000 microarray experiments curated from over 260 independent studies. Note: The manufacturer updates Oncomine (database) on a quarterly basis, doubling the database annually. Drug Treatment Data - OCM contains concepts from drug over- expression and under-expression signatures derived from 379+ compound treatment experiments spanning 164 unique compounds, many of which are FDA approved drugs. Additional Data Sources - 1) Chromosome arm and cytoband mappings; 2) Biological process, molecular function, and cellular component annotations; 3) Metabolic pathways; 4) Signaling pathways; 5) Protein domains and family assignments; 6) Protein-protein interaction sets; 7) Peer-reviewed publications resulting in over 485 literature-defined concepts. Data Analysis - OCM uses association analysis to calculate the pair- wise association of each individual concept with respect to every other concept in the database. Pairs of concepts that exhibit statistically significant overlap are considered ‘linked’. The OCM database is a growing collection of over 290,000 associations between different molecular concepts that have been detected and ranked by statistical significance. OCM enables you to upload proprietary gene signatures and identify matches of those signatures with all the concepts in the OCM database. Data Visualization - The OCM user interface is a database-driven web application providing you with the ability to navigate, analyze, and visualize molecular concepts and concept links. You have the ability to search concepts in the database by keyword, query significant concept links, and visualize networks of concept relationships. Possible questions you can answer with OCM - 1) I know the gene signature of my lead compound. What other diseases are associated with it? 2) I know the gene signature of a competitor’s compound. What pathways does it regulate? 3) I know the gene signature of my lead compound from animal studies. What other compounds are most like it? Are any of them associated with toxicological outcome in humans? 4) I am working on a diagnostic for papillary carcinoma. What genes distinguish it from clear cell carcinoma? What genes would predict both? In what other conditions are the same genes up-regulated? 5) I have a curious gene signature. What pathways and diseases are associated with those genes? Benefits - 1) Converts large amounts of high-throughput molecular data to a series of biological concepts linked by common gene expression patterns; 2) Enables the validation of current hypotheses by allowing you to compare gene lists of interest against concepts available in the OCM database; 3) Enables the building of novel hypotheses by revealing links between gene lists of interest and other biological processes; 4) Provides a broad understanding of the activated and repressed processes, pathways, and regulatory programs typical of different disease states; 5) Identifies connections between a wide range of biological phenomena, including transcriptional regulation, protein-protein interactions, disease subpopulations, and drug treatments.
Operating system configuration Microsoft Windows™ XP Professional, Version 2002, Service Pack 2 Browser configuration Microsoft® Internet Explorer® 7 as well as version 6 Version 7.0.5730.11 Cipher Strength: 128-bit Settings: Internet Zone Security level for this zone: Medium-high Cookies: Accept Session Cookies. Accept First-Party Cookies Use SSL 3.0 JavaScript must be enabled. SVG viewer Adobe™ SVG Viewer 3.0 Other configuration notes Use of Oncomine does not typically require additional system memory beyond normal web-based applications, a lack of memory may cause performance degradation and instability in Microsoft Windows. Use of Oncomine with Mozilla Firefox® is not recommended due to errors which occur in the SVG viewer. Use of Oncomine along with Google® Web Accelerator is not recommended as caching results in a failure to update views. We do not have reports of success using Oncomine on Apple platforms. A number of limitations have been observed.
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Price Contact manufacturer G6G Product Number 20015 G6G Manufacturer Number 100644 |
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