ESCAPE: Database for integrating high-content published data collected from human and mouse embryonic stem cells

Database

Volumn 2013, Issue , 2013, Pages

  Xu, Huilei ^a   Baroukh, Caroline ^a   Dannenfelser, Ruth ^a   Chen, Edward Y ^a   Tan, Christopher M ^a   Kou, Yan ^a   Kim, Yujin E ^a   Lemischka, Ihor R ^a   Ma'ayan, Avi ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ANIMAL; ARTICLE; CELL LINEAGE; CYTOLOGY; DATA BASE; EMBRYONIC STEM CELL; HIGH THROUGHPUT SCREENING; HUMAN; METABOLISM; MOUSE; PLURIPOTENT STEM CELL; PUBLICATION; SEARCH ENGINE;

ANIMALS; BIOLOGICAL MARKERS; CELL LINEAGE; DATABASES AS TOPIC; EMBRYONIC STEM CELLS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MICE; PLURIPOTENT STEM CELLS; PUBLICATIONS; SEARCH ENGINE;

EID: 84885936051     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat045     Document Type: Article

References (26)

1. Som,A., Harder,C., Greber,B. et al. (2010) The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PLoS One, 5, e15165.
2. Muller,F.J., Laurent,L.C., Kostka,D. et al. (2008) Regulatory networks define phenotypic classes of human stem cell lines. Nature, 455, 401-405.
3. Assou,S., Le Carrour,T., Tondeur,S. et al. (2007) A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas. Stem Cells, 25, 961-973.
4. Schulz,H., Kolde,R., Adler,P. et al. (2009) The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS One, 4, e6804.
5. Porter,C.J., Palidwor,G.A., Sandie,R. et al. (2007) StemBase: a resource for the analysis of stem cell gene expression data. Methods Mol. Biol., 407, 137-148.
6. Glauche,I., Herberg,M. and Roeder,I. (2010) Nanog variability and pluripotency regulation of embryonic stem cells - insights from a mathematical model analysis. PLoS One, 5, e11238.
7. Chickarmane,V., Troein,C., Nuber,U.A. et al. (2006) Transcriptional Dynamics of the embryonic stem cell switch. PLoS Comput. Biol., 2, e123.
8. MacArthur,B.D., Please,C.P. and Oreffo,R.O.C. (2008) Stochasticity and the molecular mechanisms of induced pluripotency. PLoS One, 3, e3086.
9. Xu,H., Schaniel,C., Lemischka,I.R. and Ma'ayan,A. (2010) Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev. Syst. Biol. Med., 2, 708-733.
10. Yu,J., Xing,X., Zeng,L. et al. (2012) SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research. PLoS One, 7, e35230.
11. Lopes,C.T., Franz,M., Kazi,F. et al. (2010) Cytoscape web: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.
12. Bostock,M., Ogievetsky,V. and Heer,J. (2011) D3 data-driven documents. IEEE Trans. Vis. Comput. Graph., 17, 2301-2309.
13. Holzinger,A., Mayr,S., Slany,W. and Debevc,M. (2010) The influence of AJAX on Web Usability. In: ICE-B 2010 - Proceedings of the International Conference on e-Business, ICETE The International Joint Conference on e-Business and Telecommunications. INSTICC, Athens, Greece. pp. 124-127.
14. Chen,E.Y., Tan,C.M., Kou,Y. et al. (2013) Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics, 14, 128.
15. Berger,S., Posner,J. and Ma'ayan,A. (2007) Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics, 8, 372.
16. Kohl,M., Wiese,S. and Warscheid,B. (2011) Cytoscape: software for visualization and analysis of biological networks. Methods Mol. Biol., 696, 291-303.
17. Clark,N.R., Dannenfelser,R., Tan,C.M. et al. (2012) Sets2Networks: network inference from repeated observations of sets. BMC Systems Biol., 6, 89.
18. Smith,C.L., Goldsmith,C.A. and Eppig,J.T. The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol., 6, R7.
19. He,J.C., Chuang,P.Y., Ma'Ayan,A. and Iyengar,R. (2011) Systems biology of kidney diseases. Kidney Int., 81, 22-39.
20. Xu,H., Lemischka,I.R. and Ma'ayan,A. (2010) SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst. Biol., 4, 173.
21. Kim,J., Chu,J., Shen,X. et al. An extended transcriptional network for pluripotency of embryonic stem cells. Cell, 132, 1049-1061.
22. Yang,J., Gao,C., Chai,L. and Ma,Y. (2010) A novel SALL4/OCT4 transcriptional feedback network for pluripotency of embryonic stem cells. PLoS One, 5, e10766.
23. Ding,Q., Motoyama,J., Gasca,S. et al. (1998) Diminished Sonic hedgehog signaling and lack of floor plate differentiation in Gli2 mutant mice. Development, 125, 2533-2543.
24. Po,A., Ferretti,E., Miele,E. et al. (2010) Hedgehog controls neural stem cells through p53-independent regulation of Nanog. EMBO J., 29, 2646-2658.
25. Yang,S.H., Kalkan,T., Morrisroe,C. et al. (2012) A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation. PLoS Genet., 8, e1003112.
26. De Cegli,R., Iacobacci,S., Flore,G. et al. (2013) Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation. Nucleic Acids Res., 41, 711-726.