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Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TAA, Sompallae R, Krivtsov A, Shivdasani RA, Armstrong SA, Culhane AC, Correll M, Sansone SA, Hofmann O, Hide W. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res 2012; 40:D984-91. [PMID: 22121217 PMCID: PMC3245064 DOI: 10.1093/nar/gkr1051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/13/2011] [Accepted: 10/25/2011] [Indexed: 11/24/2022] Open
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.
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Affiliation(s)
- Shannan J. Ho Sui
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Kimberly Begley
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Dorothy Reilly
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Brad Chapman
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ray McGovern
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Philippe Rocca-Sera
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Eamonn Maguire
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Gabriel M. Altschuler
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Terah A. A. Hansen
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ramakrishna Sompallae
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Andrei Krivtsov
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ramesh A. Shivdasani
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Scott A. Armstrong
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Aedín C. Culhane
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Mick Correll
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Susanna-Assunta Sansone
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Oliver Hofmann
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Winston Hide
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
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14
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Schulz H, Kolde R, Adler P, Aksoy I, Anastassiadis K, Bader M, Billon N, Boeuf H, Bourillot PY, Buchholz F, Dani C, Doss MX, Forrester L, Gitton M, Henrique D, Hescheler J, Himmelbauer H, Hübner N, Karantzali E, Kretsovali A, Lubitz S, Pradier L, Rai M, Reimand J, Rolletschek A, Sachinidis A, Savatier P, Stewart F, Storm MP, Trouillas M, Vilo J, Welham MJ, Winkler J, Wobus AM, Hatzopoulos AK. The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS One 2009; 4:e6804. [PMID: 19727443 PMCID: PMC2731164 DOI: 10.1371/journal.pone.0006804] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Accepted: 07/09/2009] [Indexed: 02/07/2023] Open
Abstract
Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the “Functional Genomics in Embryonic Stem Cells” consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in “Expression Waves” and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells.
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Affiliation(s)
- Herbert Schulz
- Max-Delbrück-Center for Molecular Medicine (MDC) Berlin-Buch, Berlin, Germany
| | - Raivo Kolde
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Priit Adler
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Irène Aksoy
- INSERM U846, Stem Cell and Brain Research Institute, Bron, France
| | | | - Michael Bader
- Max-Delbrück-Center for Molecular Medicine (MDC) Berlin-Buch, Berlin, Germany
| | | | - Hélène Boeuf
- Université Bordeaux 2, CNRS-UMR 5164, Bordeaux, France
| | | | - Frank Buchholz
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Lesley Forrester
- Queens Medical Research Institute E2.47, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Domingos Henrique
- Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Lisboa, Portugal
| | - Jürgen Hescheler
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Heinz Himmelbauer
- Max-Planck-Institute of Molecular Genetics, Berlin, Germany
- Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain
| | - Norbert Hübner
- Max-Delbrück-Center for Molecular Medicine (MDC) Berlin-Buch, Berlin, Germany
| | | | | | - Sandra Lubitz
- BioInnovation Zentrum, Technische Universitaet Dresden, Dresden, Germany
| | | | - Meena Rai
- Department of Medicine -Division of Cardiovascular Medicine and Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jüri Reimand
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | | | | | - Pierre Savatier
- INSERM U846, Stem Cell and Brain Research Institute, Bron, France
| | - Francis Stewart
- BioInnovation Zentrum, Technische Universitaet Dresden, Dresden, Germany
| | - Mike P. Storm
- Department of Pharmacy and Pharmacology, Centre for Regenerative Medicine, The University of Bath, Bath, United Kingdom
| | | | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Melanie J. Welham
- Department of Pharmacy and Pharmacology, Centre for Regenerative Medicine, The University of Bath, Bath, United Kingdom
| | - Johannes Winkler
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | | | - Antonis K. Hatzopoulos
- Department of Medicine -Division of Cardiovascular Medicine and Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute of Clinical Molecular Biology and Tumor Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Munich, Germany
- * E-mail:
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