Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs
Global molecular profiling of cancers has shown broad utility in delineating pathways and processes underlying disease, in predicting prognosis and response to therapy, and in suggesting novel treatments. To gain further insights from such data, we have integrated and analyzed a comprehensive collec...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2007-05-01
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| Series: | Neoplasia: An International Journal for Oncology Research |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1476558607800959 |
| _version_ | 1811285496643452928 |
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| author | Daniel R. Rhodes Shanker Kalyana-Sundaram Scott A. Tomlins Vasudeva Mahavisno Nicole Kasper Radhika Varambally Terrence R. Barrette Debashis Ghosh Sooryanarayana Varambally Arul M. Chinnaiyan |
| author_facet | Daniel R. Rhodes Shanker Kalyana-Sundaram Scott A. Tomlins Vasudeva Mahavisno Nicole Kasper Radhika Varambally Terrence R. Barrette Debashis Ghosh Sooryanarayana Varambally Arul M. Chinnaiyan |
| author_sort | Daniel R. Rhodes |
| collection | DOAJ |
| description | Global molecular profiling of cancers has shown broad utility in delineating pathways and processes underlying disease, in predicting prognosis and response to therapy, and in suggesting novel treatments. To gain further insights from such data, we have integrated and analyzed a comprehensive collection of “molecular concepts”" representing > 2500 cancer-related gene expression signatures from Oncomine and manual curation of the literature, drug treatment signatures from the Connectivity Map, target gene sets from genome-scale regulatory motif analyses, and reference gene sets from several gene and protein annotation databases. We computed pairwise association analysis on all 13,364 molecular concepts and identified > 290,000 significant associations, generating hypotheses that link cancer types and subtypes, pathways, mechanisms, and drugs. To navigate a network of associations, we developed an analysis platform, the Molecular Concepts Map. We demonstrate the utility of the approach by highlighting molecular concepts analyses of Myc pathway activation, breast cancer relapse, and retinoic acid treatment. |
| first_indexed | 2024-04-13T02:45:51Z |
| format | Article |
| id | doaj.art-72aa2c97c49a47c1ab3497c0d1363187 |
| institution | Directory Open Access Journal |
| issn | 1476-5586 1522-8002 |
| language | English |
| last_indexed | 2024-04-13T02:45:51Z |
| publishDate | 2007-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Neoplasia: An International Journal for Oncology Research |
| spelling | doaj.art-72aa2c97c49a47c1ab3497c0d13631872022-12-22T03:06:02ZengElsevierNeoplasia: An International Journal for Oncology Research1476-55861522-80022007-05-019544345410.1593/neo.07292Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and DrugsDaniel R. Rhodes0Shanker Kalyana-Sundaram1Scott A. Tomlins2Vasudeva Mahavisno3Nicole Kasper4Radhika Varambally5Terrence R. Barrette6Debashis Ghosh7Sooryanarayana Varambally8Arul M. Chinnaiyan9Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USAGlobal molecular profiling of cancers has shown broad utility in delineating pathways and processes underlying disease, in predicting prognosis and response to therapy, and in suggesting novel treatments. To gain further insights from such data, we have integrated and analyzed a comprehensive collection of “molecular concepts”" representing > 2500 cancer-related gene expression signatures from Oncomine and manual curation of the literature, drug treatment signatures from the Connectivity Map, target gene sets from genome-scale regulatory motif analyses, and reference gene sets from several gene and protein annotation databases. We computed pairwise association analysis on all 13,364 molecular concepts and identified > 290,000 significant associations, generating hypotheses that link cancer types and subtypes, pathways, mechanisms, and drugs. To navigate a network of associations, we developed an analysis platform, the Molecular Concepts Map. We demonstrate the utility of the approach by highlighting molecular concepts analyses of Myc pathway activation, breast cancer relapse, and retinoic acid treatment.http://www.sciencedirect.com/science/article/pii/S1476558607800959Cancerbioinformaticsgene expression signaturenetworkoncomine |
| spellingShingle | Daniel R. Rhodes Shanker Kalyana-Sundaram Scott A. Tomlins Vasudeva Mahavisno Nicole Kasper Radhika Varambally Terrence R. Barrette Debashis Ghosh Sooryanarayana Varambally Arul M. Chinnaiyan Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs Neoplasia: An International Journal for Oncology Research Cancer bioinformatics gene expression signature network oncomine |
| title | Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs |
| title_full | Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs |
| title_fullStr | Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs |
| title_full_unstemmed | Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs |
| title_short | Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs |
| title_sort | molecular concepts analysis links tumors pathways mechanisms and drugs |
| topic | Cancer bioinformatics gene expression signature network oncomine |
| url | http://www.sciencedirect.com/science/article/pii/S1476558607800959 |
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