Journal article
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons
Nucleic acids research, Vol.40(D1), pp.D984-D991
01/01/2012
DOI: 10.1093/nar/gkr1051
PMCID: PMC3245064
PMID: 22121217
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.
Details
- Title: Subtitle
- The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons
- Creators
- Shannan J. Ho Sui - Harvard UniversityKimberly Begley - Dana-Farber Cancer InstituteDorothy Reilly - Dana-Farber Cancer InstituteBrad Chapman - Dana-Farber Cancer InstituteRay McGovern - Dana-Farber Cancer InstitutePhilippe Rocca-Sera - Dana-Farber Cancer InstituteEamonn Maguire - Dana-Farber Cancer InstituteGabriel M. Altschuler - Dana-Farber Cancer InstituteTerah A. A. Hansen - Dana-Farber Cancer InstituteRamakrishna Sompallae - Harvard UniversityAndrei Krivtsov - Dana-Farber Cancer InstituteRamesh A. Shivdasani - Dana-Farber Cancer InstituteScott A. Armstrong - Dana-Farber Cancer InstituteAedin C. Culhane - Dana-Farber Cancer InstituteMick Correll - Dana-Farber Cancer InstituteSusanna-Assunta Sansone - Novartis Inst BioMed Res, Cambridge, MA USAOliver Hofmann - Harvard UniversityWinston Hide - Harvard Stem Cell Institute
- Resource Type
- Journal article
- Publication Details
- Nucleic acids research, Vol.40(D1), pp.D984-D991
- Publisher
- Oxford Univ Press
- DOI
- 10.1093/nar/gkr1051
- PMID
- 22121217
- PMCID
- PMC3245064
- ISSN
- 0305-1048
- eISSN
- 1362-4962
- Number of pages
- 8
- Grant note
- Harvard School of Public Health BB/I000771/1; BB/I025840/1; BB/E025080/1 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) Harvard Stem Cell Institute 1RC2CA148222-01 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA BB/I025840/1; BB/I000771/1; BB/E025080/1 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC)
- Language
- English
- Date published
- 01/01/2012
- Academic Unit
- Pathology
- Record Identifier
- 9984622057002771
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