ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO

Bioinformatics

Volumn 30, Issue 23, 2014, Pages 3379-3386

  Ni, Ming ^a   Ye, Fuqiang ^a   Zhu, Juanjuan ^a,b   Li, Zongwei ^a   Yang, Shuai ^a   Yang, Bite ^a   Han, Lu ^a   Wu, Yongge ^b   Chen, Ying ^a   Li, Fei ^a   Wang, Shengqi ^a,c   Bo, Xiaochen ^a  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^b JILIN UNIVERSITY   (China)

^c HENAN UNIVERSITY OF CHINESE MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; CELL HYPOXIA; CLUSTER ANALYSIS; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; MOUSE; PROCEDURES;

ANIMALS; CELL HYPOXIA; CLUSTER ANALYSIS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; INTERNET; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 84925557905     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu560     Document Type: Article

References (39)

1. Becker, C.M. et al. (2008) 2-methoxyestradiol inhibits hypoxia-inducible factor-1{alpha} and suppresses growth of lesions in a mouse model of endometriosis. Am. J. Pathol., 172, 534-544.
2. Beyer, S. et al. (2008) The histone demethylases JMJD1A and JMJD2B are transcriptional targets of hypoxia-inducible factor HIF. J. Biol. Chem., 283, 36542-36552.
3. Brahimi-Horn, M.C. et al. (2007) Hypoxia and cancer. J. Mol. Med. (Berl), 85, 1301-1307.
4. Brown, J.M. and Wilson, W.R. (2004) Exploiting tumour hypoxia in cancer treatment. Nat. Rev. Cancer, 4, 437-447.
5. Chen, R. et al. (2008) GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics, 9, 548.
6. Diaconis, P. and Graham, R. (1977) Spearman's footrule as a measure of disarray. J. R. Stat. Soc., 39, 262-268.
7. Dudley, J.T. et al. (2011) Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci. Transl. Med., 3, 96ra76.
8. Edgar, R. et al. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
9. Elvidge, G.P. et al. (2006) Concordant regulation of gene expression by hypoxia and 2-oxoglutarate-dependent dioxygenase inhibition: the role of HIF-1alpha, HIF-2alpha, and other pathways. J. Biol. Chem., 281, 15215-15226.
10. Fan, G.B. et al. (2012) Changes of oxygen content in facial skin before and after cigarette smoking. Skin Res. Technol., 18, 511-515.
11. Feng, C. et al. (2009) GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. BMC Genomics, 10, 411.
12. Frey, B.J. and Dueck, D. (2007) Clustering by passing messages between data points. Science, 315, 972-976.
13. Hoff, C.M. et al. (2012) Effect of smoking on oxygen delivery and outcome in patients treated with radiotherapy for head and neck squamous cell carcinoma-a prospective study. Radiother Oncol., 103, 38-44.
14. Hoheisel, J.D. (2006) Microarray technology: beyond transcript profiling and genotype analysis. Nat. Rev. Genet., 7, 200-210.
15. Hollander, M. and Wolfe, D.A. (1973) Nonparametric Statistical Methods. Wiley, New York.
16. Iorio, F. et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc. Natl Acad. Sci. USA, 107, 14621-14626.
17. Jensen, J.A. et al. (1991) Cigarette smoking decreases tissue oxygen. Arch. Surg., 126, 1131-1134.
18. Klapperich, C.M. and Bertozzi, C.R. (2004) Global gene expression of cells attached to a tissue engineering scaffold. Biomaterials, 25, 5631-5641.
19. Klatte, T. et al. (2007) Hypoxia-inducible factor 1 alpha in clear cell renal cell carcinoma. Clin. Cancer Res., 13, 7388-7393.
20. Lamb, J. (2007) The connectivity map: a new tool for biomedical research. Nat. Rev. Cancer, 7, 54-60.
21. Lamb, J. et al. (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929-1935.
22. Lamb, J. et al. (2003) A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell, 114, 323-334.
23. Letunic, I. and Bork, P. (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics, 23, 127-128.
24. Letunic, I. and Bork, P. (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res., 39, W475-W478.
25. Li, F. et al. (2013) GeneExpressionSignature: an R package for discovering functional connections using gene expression signatures. Omics, 17, 116-118.
26. Liberzon, A. et al. (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-1740.
27. Lin, S. (2010) Space oriented rank-based data integration. Stat. Appl. Genet. Mol. Biol., 9, Article20.
28. Plaisier, S.B. et al. (2010) Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res, 38, e169.
29. Semenza, G.L. (2007) Hypoxia and cancer. Cancer Metastasis Rev., 26, 223-224.
30. Sirota, M. et al. (2011) Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci. Transl. Med., 3, 96ra77.
31. Sorensen, L.T. et al. (2009) Acute effects of nicotine and smoking on blood flow, tissue oxygen, and aerobe metabolism of the skin and subcutis. J. Surg. Res., 152, 224-230.
32. Subramanian, A. et al. (2007) GSEA-P: a desktop application for gene set enrichment analysis. Bioinformatics, 23, 3251-3253.
33. Subramanian, A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
34. Thomas, P.D. et al. (2003) PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res., 31, 334-341.
35. Vaupel, P. and Mayer, A. (2007) Hypoxia in cancer: significance and impact on clinical outcome. Cancer Metastasis Rev., 26, 225-239.
36. Vazquez, M. et al. (2010) MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Res., 38, W228-W232.
37. Wu, J. et al. (2009) Web-based interrogation of gene expression signatures using EXALT. BMC Bioinformatics, 10, 420.
38. Yi, Y. et al. (2007) Strategy for encoding and comparison of gene expression signatures. Genome Biol., 8, R133.
39. Yu, Y. et al. (2009) GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics, 10, 264.