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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
The stem cell discovery engine: An integrated repository and analysis system for cancer stem cell comparisons
Nucleic Acids Research, Volume 40, No. D1, Year 2012
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Description
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. © The Author(s) 2011. Published by Oxford University Press.
Authors & Co-Authors
Ho Sui, Shannan J.
United States, Boston
Harvard T.h. Chan School of Public Health
Reilly, Dorothy S.
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Cambridge
Novartis Institutes for Biomedical Research, Inc.
Chapman, Brad A.
United States, Boston
Harvard T.h. Chan School of Public Health
Altschuler, Gabriel M.
United States, Boston
Harvard T.h. Chan School of Public Health
Armstrong, Scott A.
United States, Boston
Harvard Medical School
United States, Boston
Dana-farber Cancer Institute
United States, Cambridge
Harvard Stem Cell Institute
Culhane, Aedín C.
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Boston
Dana-farber Cancer Institute
Sansone, Susanna Assunta
United States, Cambridge
Novartis Institutes for Biomedical Research, Inc.
Hofmann, Oliver M.
United States, Boston
Harvard T.h. Chan School of Public Health
Hide, Winston A.
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Cambridge
Harvard Stem Cell Institute
Statistics
Citations: 19
Authors: 9
Affiliations: 6
Identifiers
Doi:
10.1093/nar/gkr1051
ISSN:
13624962
Research Areas
Cancer
Genetics And Genomics