Semantic integration of data on transcriptional regulation

Bioinformatics

Volumn 26, Issue 13, 2010, Pages 1651-1661

  Baitaluk, Michael ^a   Ponomarenko, Julia ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; PROKARYOTA;

ARTICLE; BIOLOGY; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; METHODOLOGY;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; TRANSCRIPTION, GENETIC;

EID: 77954202092     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq231     Document Type: Article

References (64)

1. Ait-ghezala,G. et al. (2008) Diagnostic utility of APOE, soluble CD40, CD40L, and Abeta1-40 levels in plasma in Alzheimer's disease. Cytokine, 44, 283-287.
2. Baitaluk,M. et al. (2006a) PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinformatics, 7, 55.
3. Baitaluk,M. et al. (2006b) BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res., 34, W466-W471.
4. Baranowska-Bik,A. et al. (2008) Plasma beta amyloid and cytokine profile in women with Alzheimer's disease. Neuro Endocrinol. Lett., 29, 75-79.
5. Baumbach,J. (2007) CoryneRegNet 4.0-Areference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8, 429.
6. Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
7. Berman,H.M. et al. (2002) The Nucleic Acid Database. Acta Crystallogr. D Biol. Crystallogr., 58, 889-898.
8. Birkland,A. and Yona,G. (2006) BIOZON: a system for unification, management and analysis of heterogeneous biological data. BMC Bioinformatics, 7, 70.
9. Birney,E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
10. Bonizzi,G. and Karin,M. (2004) The two NF-kappaB activation pathways and their role in innate and adaptive immunity. Trends Immunol., 25, 280-288.
11. Cenini,G. et al. (2008) Elevated levels of pro-apoptotic p53 and its oxidative modification by the lipid peroxidation product, HNE, in brain from subjects with amnestic mild cognitive impairment and Alzheimer's disease. J. Cell. Mol. Med., 12, 987-994.
12. Cerami,E.G. et al. (2006) cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics, 7, 497.
13. Chelala,C. et al. (2009) SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics, 25, 655-661.
14. Cochrane,G.R. and Galperin,M.Y. (2010) The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. Nucleic Acids Res., 38, D1-D4.
15. Davidson,S.B. et al. (2001) K2Kleisli and GUS: experiments in integrated access to genomic data sources. IBM Syst. J., 40, 512-530.
16. Davuluri,R.V. et al. (2003) AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics, 4, 25.
17. Drysdale,R. (2008) FlyBase: a database for the Drosophila research community. Methods Mol. Biol., 420, 45-59.
18. Egaña,M. et al. (2008) In situ migration of handcrafted ontologies to reason-able forms. Data Knowl. Eng., 66, 147-162.
19. Elluru,S.R. et al. (2008) Induction of maturation and activation of human dendritic cells: a mechanism underlying the beneficial effect of Viscum album as complimentary therapy in cancer. BMC Cancer, 8, 161.
20. Etzold,T. and Argos,P. (1993) SRS-an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci., 9, 49-57.
21. Farach-Colton,M. et al. (2000) On the sorting-complexity of suffix tree construction. J. Assoc. Comput. Mach., 47, 987-1011.
22. Finn,R.D. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
23. Gatta,L. et al. (2009) Peripheral blood mononuclear cells from mild cognitive impairment patients show deregulation of Bax and Sod1 mRNAs. Neurosci. Lett., 453, 36-40.
24. Giardine,B. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
25. Giegerich,R. et al. (2003) Efficient implementation of lazy suffix trees. Softw. Pract. Exp., 33, 1035-1049.
26. Good,B.M. and Wilkinson,M.D. (2006) The Life Sciences Semantic Web is full of creeps! Brief. Bioinform., 7, 275-286.
27. Gordin,D. et al. (2008) Acute hyperglycaemia induces an inflammatory response in young patients with type 1 diabetes. Ann. Med., 40, 627-633.
28. Granic,I. et al. (2009) Inflammation and NF-kappaB in Alzheimer's disease and diabetes. J. Alzheimers Dis., 16, 809-821.
29. Griffith,O.L. et al. (2008) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res., 36, D107-D113.
30. Grimm,T. et al. (2005) EBV latent membrane protein-1 protects B cells from apoptosis by inhibition of BAX. Blood, 105, 3263-3269.
31. Grumbling,G. and Strelets,V. (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res., 34, D484-D488.
32. Gusfield,D. (1997) Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press.
33. Haider,S. et al. (2009) BioMart Central Portal-unified access to biological data. Nucleic Acids Res., 37, W23-W27.
34. Hermoso,A. et al. (2004) TrSDB: a proteome database of transcription factors. Nucleic Acids Res., 32, D171-D173.
35. Hijikata,A. et al. (2007) Construction of an open-access database that integrates crossreference information from the transcriptome and proteome of immune cells. Bioinformatics, 23, 2934-2941.
36. Hoffmann,A. et al. (2006) Transcriptional regulation via the NF-kappaB signaling module. Oncogene, 25, 6706-6716.
37. Hu,Z. et al. (2007) Towards zoomable multidimensional maps of the cell. Nat. Biotechnol., 25, 547-554.
38. Hubbard,T.J. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
39. Hulo,N. et al. (2006) The PROSITE database. Nucleic Acids Res., 34, D227-D230.
40. Jeong,S.J. et al. (2004) HTLV-I Tax induces a novel interaction between p65/RelA and p53 that results in inhibition of p53 transcriptional activity. Blood, 104, 1490-1497.
41. Jones,P. et al. (2008) PRIDE: new developments and new datasets. Nucleic Acids Res., 36, D878-D883.
42. Kohler,J. et al. (2006) Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics, 22, 1383-1390.
43. Kolchanov,N.A. et al. (2002) Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res., 30, 312-317.
44. Kolchanov,N.A. et al. (1999) Integrated databases and computer systems for studying eukaryotic gene expression. Bioinformatics, 15, 669-686.
45. Kummerfeld,S.K. and Teichmann,S.A. (2006) DBD: a transcription factor prediction database. Nucleic Acids Res., 34, D74-D81.
46. Kuntzer,J. et al. (2007) BNDB-the Biochemical Network Database. BMC Bioinformatics, 8, 367.
47. Laibe,C. and Le Novere,N. (2007) MIRIAM resources: tools to generate and resolve robust cross-references in systems biology. BMC Syst. Biol., 1, 58.
48. Matys,V. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
49. May,P. et al. (2009) ChlamyCyc: an integrative systems biology database andweb-portal for Chlamydomonas reinhardtii. BMC Genomics, 10, 209.
50. Murphy,T.L. et al. (1995) Regulation of interleukin 12 p40 expression through an NFkappa B half-site. Mol. Cell. Biol., 15, 5258-5267.
51. Page,L. et al. (1999) The PageRank citation ranking: bringing order to the web. Technical Report. Stanford InfoLab.
52. Pruess,M. et al. (2005) The Integr8 project-a resource for genomic and proteomic data. In Silico Biol., 5, 179-185.
53. Ruttenberg,A. et al. (2007) Advancing translational research with the Semantic Web. BMC Bioinformatics, 8, S2.
54. Sayers,E.W. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
55. Shah,S.P. et al. (2005) Atlas-a data warehouse for integrative bioinformatics. BMC Bioinformatics, 6, 34.
56. Shakhov,A.N. et al. (1990) Structural analysis of the rabbit TNF locus, containing the genes encoding TNF-beta (lymphotoxin) and TNF-alpha (tumor necrosis factor). Gene, 95, 215-221.
57. Sharma,R. et al. (2004) Prognostic significance of stromelysin-3 and tissue inhibitor of matrix metalloproteinase-2 in esophageal cancer. Oncology, 67, 300-309.
58. Siepel,A. et al. (2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17, 83-94.
59. Subramaniam,S. (1998) The Biology Workbench-a seamless database and analysis environment for the biologist. Proteins, 32, 1-2.
60. Szoke,D. et al. (2009) Polymorphisms of the ApoE, HSD3B1, IL-1beta and p53 genes are associated with the development of early uremic complications in diabetic patients: results of a DNAresequencing array study. Int. J. Mol. Med., 23, 217-227.
61. Varo,N. et al. (2003) Elevated plasma levels of the atherogenic mediator soluble CD40 ligand in diabetic patients: a novel target of thiazolidinediones. Circulation, 107, 2664-2669.
62. Verkoczy,L. et al. (2005) A role for nuclear factor kappa B/rel transcription factors in the regulation of the recombinase activator genes. Immunity, 22, 519-531.
63. Vogel,C.F. and Matsumura,F. (2009) A new cross-talk between the aryl hydrocarbon receptor and RelB, a member of the NF-kappaB family. Biochem. Pharmacol., 77, 734-745.
64. Vogel,C.F. et al. (2007) Involvement of RelB in aryl hydrocarbon receptor-mediated induction of chemokines. Biochem. Biophys. Res. Commun., 363, 722-726.