The stem cell discovery engine: An integrated repository and analysis system for cancer stem cell comparisons

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Sui, Shannan J Ho ^a   Begley, Kimberly ^a   Reilly, Dorothy ^a,b   Chapman, Brad ^a   McGovern, Ray ^a   Rocca Sera, Philippe ^c   Maguire, Eamonn ^c   Altschuler, Gabriel M ^a   Hansen, Terah A A ^a   Sompallae, Ramakrishna ^a   Krivtsov, Andrei ^d,e   Shivdasani, Ramesh A ^e,f   Armstrong, Scott A ^d,e,f   Culhane, Aedín C ^a,g   Correll, Mick ^g   Sansone, Susanna Assunta ^b   Hofmann, Oliver ^a   Hide, Winston ^a,f  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d BOSTON CHILDREN S HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f HARVARD STEM CELL INSTITUTE   (United States)

^g DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BLOOD; BRAIN; CANCER STEM CELL; COMPUTER INTERFACE; DATA PROCESSING; FACTUAL DATABASE; INTESTINE; MOLECULAR GENETICS; PRIORITY JOURNAL; SEARCH ENGINE; STEM CELL DISCOVERY ENGINE;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; MICE; NEOPLASTIC STEM CELLS; SYSTEMS INTEGRATION;

EID: 84862200196     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1051     Document Type: Article

References (25)

1. Dick,J.E. (2008) Stem cell concepts renew cancer research. Blood, 112, 4793-4807.
2. Reya,T., Morrison,S.J., Clarke,M.F. and Weissman,I.L. (2001) Stem cells, cancer, and cancer stem cells. Nature, 414, 105-111. (Pubitemid 33041634)
3. Bao,S., Wu,Q., McLendon,R.E., Hao,Y., Shi,Q., Hjelmeland,A.B., Dewhirst,M.W., Bigner,D.D. and Rich,J.N. (2006) Glioma stem cells promote radioresistance by preferential activation of the DNA damage response. Nature, 444, 756-760. (Pubitemid 44949604)
4. Ben-Porath,I., Thomson,M.W., Carey,V.J., Ge,R., Bell,G.W., Regev,A. and Weinberg,R.A. (2008) An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat. Genet., 40, 499-507. (Pubitemid 351601215)
5. Kappadakunnel,M., Eskin,A., Dong,J., Nelson,S.F., Mischel,P.S., Liau,L.M., Ngheimphu,P., Lai,A., Cloughesy,T.F., Goldin,J. et al. (2010) Stem cell associated gene expression in glioblastoma multiforme: relationship to survival and the subventricular zone. J. Neurooncol., 96, 359-367.
6. Onaitis,M., D'Amico,T.A., Clark,C.P., Guinney,J., Harpole,D.H. and Rawlins,E.L. (2011) A 10-gene progenitor cell signature predicts poor prognosis in lung adenocarcinoma. Ann. Thorac. Surg., 91, 1046-1050; discussion 1050.
7. Pece,S., Tosoni,D., Confalonieri,S., Mazzarol,G., Vecchi,M., Ronzoni,S., Bernard,L., Viale,G., Pelicci,P.G. and Di Fiore,P.P. (2010) Biological and molecular heterogeneity of breast cancers correlates with their cancer stem cell content. Cell, 140, 62-73.
8. Varnat,F., Duquet,A., Malerba,M., Zbinden,M., Mas,C., Gervaz,P. and Ruiz i Altaba,A. (2009) Human colon cancer epithelial cells harbour active HEDGEHOG-GLI signalling that is essential for tumour growth, recurrence, metastasis and stem cell survival and expansion. EMBO Mol. Med., 1, 338-351.
9. Sjolund,J., Manetopoulos,C., Stockhausen,M.T. and Axelson,H. (2005) The Notch pathway in cancer: differentiation gone awry. Eur. J. Cancer, 41, 2620-2629. (Pubitemid 41607552)
10. Yang,L., Bian,Y., Huang,S., Ma,X., Zhang,C., Su,X., Chen,Z.J., Xie,J. and Zhang,H. (2011) Identification of signature genes for detecting hedgehog pathway activation in esophageal cancer. Pathol. Oncol. Res., 17, 387-391.
11. Rocca-Serra,P., Brandizi,M., Maguire,E., Sklyar,N., Taylor,C., Begley,K., Field,D., Harris,S., Hide,W., Hofmann,O. et al. (2010) ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics, 26, 2354-2356.
12. Blankenberg,D., Von Kuster,G., Coraor,N., Ananda,G., Lazarus,R., Mangan,M., Nekrutenko,A. and Taylor,J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol., Chapter 19, Unit 19 10 11-21.
13. Goecks,J., Nekrutenko,A. and Taylor,J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
14. Culhane,A.C., Schwarzl,T., Sultana,R., Picard,K.C., Picard,S.C., Lu,T.H., Franklin,K.R., French,S.J., Papenhausen,G., Correll,M. et al. (2010) GeneSigDB-a curated database of gene expression signatures. Nucleic Acids Res., 38, D716-725.
15. Liberzon,A., Subramanian,A., Pinchback,R., Thorvaldsdottir,H., Tamayo,P. and Mesirov,J.P. (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-1740.
16. Pico,A.R., Kelder,T., van Iersel,M.P., Hanspers,K., Conklin,B.R. and Evelo,C. (2008) WikiPathways: pathway editing for the people. PLoS Biol., 6, e184.
17. Gaudet,P., Bairoch,A., Field,D., Sansone,S.A., Taylor,C., Attwood,T.K., Bateman,A., Blake,J.A., Bult,C.J., Cherry,J.M. et al. (2011) Towards BioDBcore: a community-defined information specification for biological databases. Database, 2011, baq027.
18. Brazma,A. (2009) Minimum Information About a Microarray Experiment (MIAME)-successes, failures, challenges. ScientificWorldJournal, 9, 420-423.
19. Sansone,S.A., Rocca-Serra,P., Field,D., Maguire,E., Taylor,C., Hide,W., Hofmann,O., Fang,H., Neumann,S., Tong,T. et al. (2011) Towards interoperable bioscience data. Nature Genetics., in press.
20. Whetzel,P.L., Noy,N.F., Shah,N.H., Alexander,P.R., Nyulas,C., Tudorache,T. and Musen,M.A. (2011) BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res., 39, W541-W545.
21. Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M., Marshall,K.A. et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res., 37, D885-D890.
22. Sansone,S.A., Rocca-Serra,P., Brandizi,M., Brazma,A., Field,D., Fostel,J., Garrow,A.G., Gilbert,J., Goodsaid,F., Hardy,N. et al. (2008) The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". Omics, 12, 143-149. (Pubitemid 351873437)
23. Porter,C.J., Palidwor,G.A., Sandie,R., Krzyzanowski,P.M., Muro,E.M., Perez-Iratxeta,C. and Andrade-Navarro,M.A. (2007) StemBase: a resource for the analysis of stem cell gene expression data. Methods Mol. Biol., 407, 137-148.
24. Sandie,R., Palidwor,G.A., Huska,M.R., Porter,C.J., Krzyzanowski,P.M., Muro,E.M., Perez-Iratxeta,C. and Andrade- Navarro,M.A. (2009) Recent developments in StemBase: a tool to study gene expression in human and murine stem cells. BMC Res. Notes, 2, 39.
25. Bard,J., Rhee,S.Y. and Ashburner,M. (2005) An ontology for cell types. Genome Biol., 6, R21.