The Stem Cell Discovery Engine: An Integrated Repository and Analysis System for Cancer Stem Cell Comparisons

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The Stem Cell Discovery Engine: An Integrated Repository and Analysis System for Cancer Stem Cell Comparisons

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Title: The Stem Cell Discovery Engine: An Integrated Repository and Analysis System for Cancer Stem Cell Comparisons
Author: Begley, Kimberly; Reilly, Dorothy; McGovern, Ray; Rocca-Sera, Philippe; Maguire, Eamonn; Altschuler, Gabriel M.; Culhane, Aedín C.; Correll, Mick; Sansone, Susanna-Assunta; Ho Sui, Shannan; Chapman, Brad Alan; Hansen, Terah; Sompallae, Ramakrishna Rao; Krivtsov, Andrei V.; Shivdasani, Ramesh Arjun; Armstrong, Scott A.; Hofmann, Oliver Marc; Hide, Winston

Note: Order does not necessarily reflect citation order of authors.

Citation: Ho Sui, Shannan J., Kimberly Begley, Dorothy Reilly, Brad Chapman, Ray McGovern, Philippe Rocca-Sera, Eamonn Maguire, et al. 2011. The stem cell discovery engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Research 40(D1): D984-D991.
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Abstract: Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene and pathway signatures in cancers are inconsistent across experimental systems. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), we have developed the Stem Cell Discovery Engine (SCDE)—an online database of curated CSC experiments coupled to the Galaxy analytical framework. The SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. Our initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. The SCDE is available at http://discovery.hsci.harvard.edu.
Published Version: doi:10.1093/nar/gkr1051
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245064/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:8646706
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