Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles
DNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible or comparable. Furthermore, several important analytic approaches have been applied to microarray analysis; however, their application is often limited. To overcome...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2007-02-01
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| Series: | Neoplasia: An International Journal for Oncology Research |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1476558607800479 |
| _version_ | 1818148023075602432 |
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| author | Daniel R. Rhodes Shanker Kalyana-Sundaram Vasudeva Mahavisno Radhika Varambally Jianjun Yu Benjamin B. Briggs Terrence R. Barrette Matthew J. Anstet Colleen Kincead-Beal Prakash Kulkarni Sooryanaryana Varambally Debashis Ghosh Arul M. Chinnaiyan |
| author_facet | Daniel R. Rhodes Shanker Kalyana-Sundaram Vasudeva Mahavisno Radhika Varambally Jianjun Yu Benjamin B. Briggs Terrence R. Barrette Matthew J. Anstet Colleen Kincead-Beal Prakash Kulkarni Sooryanaryana Varambally Debashis Ghosh Arul M. Chinnaiyan |
| author_sort | Daniel R. Rhodes |
| collection | DOAJ |
| description | DNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible or comparable. Furthermore, several important analytic approaches have been applied to microarray analysis; however, their application is often limited. To overcome these limitations, we have developed Oncomine, a bioinformatics initiative aimed at collecting, standardizing, analyzing, and delivering cancer transcriptome data to the biomedical research community. Our analysis has identified the genes, pathways, and networks deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types and subtypes. Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org. |
| first_indexed | 2024-12-11T12:44:33Z |
| format | Article |
| id | doaj.art-703e4790c2df4e62af3a28ccd7693e84 |
| institution | Directory Open Access Journal |
| issn | 1476-5586 1522-8002 |
| language | English |
| last_indexed | 2024-12-11T12:44:33Z |
| publishDate | 2007-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Neoplasia: An International Journal for Oncology Research |
| spelling | doaj.art-703e4790c2df4e62af3a28ccd7693e842022-12-22T01:06:52ZengElsevierNeoplasia: An International Journal for Oncology Research1476-55861522-80022007-02-019216618010.1593/neo.07112Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression ProfilesDaniel R. Rhodes0Shanker Kalyana-Sundaram1Vasudeva Mahavisno2Radhika Varambally3Jianjun Yu4Benjamin B. Briggs5Terrence R. Barrette6Matthew J. Anstet7Colleen Kincead-Beal8Prakash Kulkarni9Sooryanaryana Varambally10Debashis Ghosh11Arul M. Chinnaiyan12Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USACompendia Bioscience, Inc., Ann Arbor, MI 48104, USACompendia Bioscience, Inc., Ann Arbor, MI 48104, USACompendia Bioscience, Inc., Ann Arbor, MI 48104, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USADNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible or comparable. Furthermore, several important analytic approaches have been applied to microarray analysis; however, their application is often limited. To overcome these limitations, we have developed Oncomine, a bioinformatics initiative aimed at collecting, standardizing, analyzing, and delivering cancer transcriptome data to the biomedical research community. Our analysis has identified the genes, pathways, and networks deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types and subtypes. Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org.http://www.sciencedirect.com/science/article/pii/S1476558607800479Oncominecancer gene expressionmicroarraysbioinformaticsdifferential expression |
| spellingShingle | Daniel R. Rhodes Shanker Kalyana-Sundaram Vasudeva Mahavisno Radhika Varambally Jianjun Yu Benjamin B. Briggs Terrence R. Barrette Matthew J. Anstet Colleen Kincead-Beal Prakash Kulkarni Sooryanaryana Varambally Debashis Ghosh Arul M. Chinnaiyan Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles Neoplasia: An International Journal for Oncology Research Oncomine cancer gene expression microarrays bioinformatics differential expression |
| title | Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles |
| title_full | Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles |
| title_fullStr | Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles |
| title_full_unstemmed | Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles |
| title_short | Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles |
| title_sort | oncomine 3 0 genes pathways and networks in a collection of 18 000 cancer gene expression profiles |
| topic | Oncomine cancer gene expression microarrays bioinformatics differential expression |
| url | http://www.sciencedirect.com/science/article/pii/S1476558607800479 |
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