Inferring genome-wide functional modulatory network: A case study on NF-κB/RelA transcription factor

Journal of Computational Biology

Volumn 22, Issue 4, 2015, Pages 300-312

  Li, Xueling ^a,b   Zhu, Min ^a,b,c   Brasier, Allan R ^a,b   Kudlicki, Andrzej S ^a,b  

^a University of Texas Medical Branch School of Medicine   (United States)

^b UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

^c HEFEI INSTITUTES OF PHYSICAL SCIENCE   (China)

Author keywords

Integrative probabilistic model; Modulator; Modulatory network; NF B; Transcription factor

Indexed keywords

RELA PROTEIN, HUMAN; TRANSCRIPTION FACTOR RELA;

BIOLOGICAL MODEL; BURN; EPITHELIAL MESENCHYMAL TRANSITION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; HUMAN; HUMAN GENOME; METABOLISM; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; TUMOR CELL LINE;

BURNS; CELL LINE, TUMOR; EPITHELIAL-MESENCHYMAL TRANSITION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENOME, HUMAN; HUMANS; MODELS, GENETIC; PROTEIN INTERACTION MAPS; TRANSCRIPTION FACTOR RELA;

EID: 84926687991     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2014.0299     Document Type: Conference Paper

References (39)

1. Abraham, E. 2003. Nuclear factor-kappaB and its role in sepsis-associated organ failure. J. Infect. Dis. 187 Suppl 2, S364-S369
2. Babur, O., Demir, E., Gonen, M., et al. 2010. Discovering modulators of gene expression. Nucleic Acids Res. 38, 5648-5656
3. Charpin, C., Arnoux, F., Martin, M., et al. 2013. New autoantibodies in early rheumatoid arthritis. Arthritis Res. Ther. 15, R78
4. Chen, F. 2005. Is NF-kappaB a culprit in type 2 diabetes? Biochem. Biophys. Res. Commun. 332, 1-3
5. Choudhary, S., Rosenblatt, K. P., Fang, L., et al. 2011. High throughput short interfering RNA (siRNA) screening of the human kinome identifies novel kinases controlling the canonical nuclear factor-kappaB (NF-kappaB) activation pathway. J. Biol. Chem. 286, 37187-37195
6. Csiszar, A., Wang, M., Lakatta, E. G., and Ungvari, Z. 2008. Inflammation and endothelial dysfunction during aging: role of NF-kappaB. J. Appl. Physiol. 105, 1333-1341
7. Drafahl, K. A., McAndrew, C. W., Meyer, A. N., et al. 2010. The receptor tyrosine kinase FGFR4 negatively regulates NF-kappaB signaling. PLoS One 5, e14412
8. Foehr, E. D., Lin, X., O'Mahony, A., et al. 2000. NF-kappa B signaling promotes both cell survival and neurite process formation in nerve growth factor-stimulated PC12 cells. J. Neurosci. 20, 7556-7563
9. Gilmore, T. D. 2006. Introduction to NF-kappaB: players, pathways, perspectives. Oncogene 25, 6680-6684
10. Green, M. R., Gandhi, M. K., Courtney, M. J., et al. 2009. Relative abundance of full-length and truncated FOXP1 isoforms is associated with differential NFkappaB activity in follicular lymphoma. Leuk. Res. 33, 1699-1702
11. Grosjean, J., Kiriakidis, S., Reilly, K., et al. 2006. Vascular endothelial growth factor signalling in endothelial cell survival: a role for NFkappaB. Biochem. Biophys. Res. Commun. 340, 984-994
12. Han, Z., Boyle, D. L., Manning, A. M., and Firestein, G. S. 1998. AP-1 and NF-kappaB regulation in rheumatoid arthritis and murine collagen-induced arthritis. Autoimmunity 28, 197-208
13. Huber, M. A., Azoitei, N., Baumann, B., et al. 2004. NF-kappaB is essential for epithelial-mesenchymal transition and metastasis in a model of breast cancer progression. J. Clin. Invest. 114, 569-581
14. Ijaz, T., Pazdrak, K., Kalita, M., et al. 2014. Systems biology approaches to understanding Epithelial Mesenchymal Transition (EMT) in mucosal remodeling and signaling in asthma. World Allergy Organ. J. 7, 13
15. Jennewein, C., Karl, S., Baumann, B., et al. 2012. Identification of a novel pro-apoptotic role of NF-kappaB in the regulation of TRAIL-and CD95-mediated apoptosis of glioblastoma cells. Oncogene 31, 1468-1474
16. Jin, H. O., Seo, S. K., Kim, Y. S., et al. 2011. TXNIP potentiates Redd1-induced mTOR suppression through stabilization of Redd1. Oncogene 30, 3792-3801
17. Jin, R., Yi, Y., Yull, F. E., et al. 2014. NF-kappaB gene signature predicts prostate cancer progression. Cancer Res. 74, 2763-2772
18. Jun, H. S., Cheung, Y. Y., Lee, Y. M., et al. 2012. Glucose-6-phosphatase-beta, implicated in a congenital neutropenia syndrome, is essential for macrophage energy homeostasis and functionality. Blood 119, 4047-4055
19. Koziol, A., Gonzalo, P., Mota, A., et al. 2012. The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells. FASEB J. 26, 4481-4494
20. Li, X., Zhao, Y., Tian, B., et al. 2014. Modulation of gene expression regulated by the transcription factor NF-kappaB/ RelA. J. Biol. Chem. 289, 11927-11944
21. Lu, A., Proto, J. D., Guo, L., et al. 2011. NF-kappaB negatively impacts the myogenic potential of muscle-derived stem cells. Mol. Ther. 20, 661-668
22. Marumo, T., Schini-Kerth, V. B., and Busse R. 1999. Vascular endothelial growth factor activates nuclear factorkappaB and induces monocyte chemoattractant protein-1 in bovine retinal endothelial cells. Diabetes 48, 1131-1137
23. Maruyama, Y., Maruyama, K., Kato, Y., et al. 2014. The effect of podoplanin inhibition on lymphangiogenesis under pathological conditions. Invest. Ophthalmol. Vis. Sci. 55, 4813-4822
24. Merk, D. R., Chin, J. T., Dake, B. A., et al. 2011. miR-29b participates in early aneurysm development in Marfan syndrome. Circ. Res. 110, 312-324
25. Miljkovic-Liciana, M., Hammel, P., Garrido-Urbani, S., et al. 2009. Sushi repeat protein X-linked 2, a novel mediator of angiogensis. FASEB J. 23, 4105-4116
26. Nair, V. S., Gevaert, O., Davidzon, G., et al. 2013. NF-kappaB protein expression associates with (18)F-FDG PET tumor uptake in non-small cell lung cancer: a radiogenomics validation study to understand tumor metabolism. Lung Cancer 83, 189-196
27. Pahl, A., and Szelenyi, I. 2002. Asthma therapy in the new millennium. Inflamm. Res. 51, 273-282
28. Pahl, H. L. 1999. Activators and target genes of Rel/NF-kappaB transcription factors. Oncogene 18, 6853-6866
29. Ramdass, B., Maliekal, T. T., Lakshmi, S., et al. 2007. Coexpression of Notch1 and NF-kappaB signaling pathway components in human cervical cancer progression. Gynecol. Oncol. 104, 352-361
30. Romashkova, J. A., and Makarov, S. S. 1999. NF-kappaB is a target of AKT in anti-apoptotic PDGF signalling. Nature 401, 86-90
31. Sartor, M. A., Mahavisno, V., Keshamouni, V. G., et al. 2010. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics 26, 456-463
32. Scatena, M., Almeida, M., Chaisson, M. L., et al. 1998. NF-kappaB mediates alphavbeta3 integrin-induced endothelial cell survival. J. Cell Biol. 141, 1083-1093
33. Vuillemenot, B. R., Kennedy, D., Cooper, J. D., et al. 2014. Nonclinical evaluation of CNS-administered TPP1 enzyme replacement in canine CLN2 neuronal ceroid lipofuscinosis. Mol. Genet. Metab. 114, 281-293
34. Wei, H. S., Wei, H. L., Zhao, F., et al. 2013. Glycosyltransferase GLT8D2 positively regulates ApoB100 protein expression in hepatocytes. Int. J. Mol. Sci. 14, 21435-21446
35. Wu, G., Feng, X., and Stein, L. 2010. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11, R53
36. Yang, J., Mitra, A., Dojer, N., et al. 2013. A probabilistic approach to learn chromatin architecture and accurate inference of the NF-jB/RelA regulatory network using ChIP-Seq. Nucleic Acids Res. 41, 7240-7259
37. Yang, W., Xia, Y., Cao, Y., et al. 2012. EGFR-induced and PKCepsilon monoubiquitylation-dependent NF-kappaB activation upregulates PKM2 expression and promotes tumorigenesis. Mol. Cell. 48, 771-784
38. Zhang, B., Liu, X., Chen, W., and Chen, L. 2013. IFIT5 potentiates anti-viral response through enhancing innate immune signaling pathways. Acta Biochim. Biophys. Sin. 45, 867-874
39. Zhou, B., Xu, W., Herndon, D., et al. 2010. Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Proc. Natl. Acad. Sci. USA 107, 9923-9928.