Leukemia gene atlas - a public platform for integrative exploration of genome-wide molecular data

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Hebestreit, Katja ^a   Gröttrup, Sören ^a   Emden, Daniel ^a   Veerkamp, Jannis ^a   Ruckert, Christian ^a   Klein, Hans Ulrich ^a   Müller Tidow, Carsten ^a   Dugas, Martin ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER GENETICS; CANCER RESEARCH; DNA METHYLATION; DNA MICROARRAY; FACTUAL DATABASE; GENE EXPRESSION; GENE SEQUENCE; HEMATOPOIESIS; INFORMATION RETRIEVAL; LEUKEMIA; LEUKEMIA GENE ATLAS; MOLECULAR GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

DATABASES, GENETIC; HUMANS; INTERNET; LEUKEMIA;

EID: 84862255345     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039148     Document Type: Article

References (26)

1. Haferlach T, Kohlmann A, Wieczorek L, Basso G, Kronnie GT, et al. (2010) Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group. J Clin Oncol. 28: 2529-37.
2. Meyerson M, Gabriel S, Getz G, (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 11: 685-96.
3. Cronin M, Ross JS, (2011) Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology. Biomark Med 5: 293-305.
4. Theilgaard-Mönch K, Boultwood J, Ferrari S, Giannopoulos K, Hernandez-Rivas JM, et al. (2011) Gene expression profiling in MDS and AML: potential and future avenues. Leukemia 25: 909-20.
5. Neff T, Armstrong SA, (2009) Chromatin maps, histone modifications and leukemia. Leukemia 23: 1243-51.
6. Klein HU, Ruckert C, Kohlmann A, Bullinger L, Thiede C, et al. (2009) Quantitative comparison of microarray experiments with published leukemia related gene expression signatures. BMC Bioinformatics 10: 422.
7. Hawkins RD, Hon GC, Ren B, (2010) Next-generation genomics: an integrative approach. Nat Rev Genet 11: 476-86.
8. PostgreSQL Avilable: http://www.postgresql.org. Accessed 2012 Mai 23.
9. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37: D885-90.
10. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing.
11. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5: R80.
12. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, et al. (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39: D945-50.
13. COSMIC Biomart website. Available: http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview. Accessed 2012 Mai 23.
14. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57: 289-300.
15. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative Genomics Viewer. Nat Biotechnol 29: 24-6.
16. Bluteau D, Gilles L, Hilpert M, Antony-Debré I, James C, et al. (2011) Down-regulation of the RUNX1-target gene NR4A3 contributes to hematopoiesis deregulation in familial platelet disorder/acute myelogenous leukemia (FPD/AML). Blood 118: 6310-20.
17. Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, et al. (2011) Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144: 296-309.
18. Tijssen MR, Cvejic A, Joshi A, Hannah RL, Ferreira R, et al. (2011) Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. Dev Cell 20: 597-609.
19. Kohlmann A, Grossmann V, Klein HU, Schindela S, Weiss T, et al. (2010) Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8% of chronic myelomonocytic leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1. J Clin Oncol 28: 3858-65.
20. Verhaak RG, Wouters BJ, Erpelinck CA, Abbas S, Beverloo HB, et al. (2009) Prediction of molecular subtypes in acute myeloid leukemia based on gene expression profiling. Haematologica 94: 131-4.
21. Gadaleta E, Lemoine NR, Chelala C, (2011) Online resources of cancer data: barriers, benefits and lessons. Brief Bioinform 12: 52-63.
22. Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, et al. (2011) ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39: D1002-4.
23. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, et al. (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9: 166-80.
24. Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, et al. (2007) The NCBI dbGaP database of genotypes and phenotypes. Nat Genet. 39: 1181-6.
25. Cancer Genome Atlas Research Network, (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-8.
26. Huret JL, Dessen P, Bernheim A, (2001) Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated. Nucleic Acids Res 29: 303-4.