Difference between revisions of "CeRNA Query"
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| − | This component provides query access to a precomputed database of competitive endogenous RNA (ceRNA) interactions, also called "sponge" interactions. These interactions underlie a post-transcriptional layer of regulation, and were predicted using the Hermes algorithm (Sumazin et al., 2011) with subsequent improvements (submitted). | + | This component provides query access to a precomputed database of competitive endogenous RNA (ceRNA) interactions, also called "sponge" interactions. These interactions underlie a post-transcriptional layer of regulation, and were predicted using the Hermes algorithm ([http://www.ncbi.nlm.nih.gov/pubmed/22000015 Sumazin et al., 2011]) with subsequent improvements (submitted). |
Datasets for Glioblastoma (GBM), Ovarian (OV), Breast (BRCA), and Prostate (PRAD) cancer are currently available. Each is calculated by analyzing gene expression profiles in combination with matched microRNA (miR) profiles obtained from the TCGA. | Datasets for Glioblastoma (GBM), Ovarian (OV), Breast (BRCA), and Prostate (PRAD) cancer are currently available. Each is calculated by analyzing gene expression profiles in combination with matched microRNA (miR) profiles obtained from the TCGA. | ||
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| − | Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell '''147'''(2):370-81. doi: 10.1016/j.cell.2011.09.041. | + | Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell '''147'''(2):370-81. doi: 10.1016/j.cell.2011.09.041 ([http://www.ncbi.nlm.nih.gov/pubmed/22000015 link to paper]). |
Revision as of 15:54, 2 August 2013
This component provides query access to a precomputed database of competitive endogenous RNA (ceRNA) interactions, also called "sponge" interactions. These interactions underlie a post-transcriptional layer of regulation, and were predicted using the Hermes algorithm (Sumazin et al., 2011) with subsequent improvements (submitted).
Datasets for Glioblastoma (GBM), Ovarian (OV), Breast (BRCA), and Prostate (PRAD) cancer are currently available. Each is calculated by analyzing gene expression profiles in combination with matched microRNA (miR) profiles obtained from the TCGA.
Hermes predicts the intersection set (program) of miRNAs which bind to both of two different RNAs. Variation in the level of one of the RNA species may affect the level of the second RNA via its effects on the availability of the various miRNAs.
Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147(2):370-81. doi: 10.1016/j.cell.2011.09.041 (link to paper).
