Genes related to differentiation are correlated with the gene regulatory network structure

Bioinformatics

Volumn 30, Issue 3, 2014, Pages 406-413

  Bodaker, Matan ^a   Meshorer, Eran ^b   Mitrani, Eduardo ^a   Louzoun, Yoram ^c  

^a Department of Cell and Developmental Biology ^*  (Israel)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^c BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CELL DIFFERENTIATION; GENE REGULATORY NETWORK; GENETICS; PROTEIN ANALYSIS;

ALGORITHMS; CELL DIFFERENTIATION; GENE REGULATORY NETWORKS; PROTEIN INTERACTION MAPPING;

EID: 84893226649     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt685     Document Type: Article

References (43)

1. Ahn, S., et al. (2009) Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybrids. PLoS Comput. Biol., 5, e1000407.
2. Alonso, L. and Fuchs, E. (2003) Stem cells of the skin epithelium. Proc. Natl Acad. Sci. USA, 100, 11830-11835.
3. Barker, N., et al. (2010) Tissue-resident adult stem cell populations of rapidly selfrenewing organs. Cell Stem Cell, 7, 656-670.
4. Bodaker, M., et al. (2013) Mathematical conditions for induced cell differentiation and trans-differentiation in adult cells. Bull. Math. Biol., 75, 819-844.
5. Cho, H.H., et al. (2009) NF-kappaB activation stimulates osteogenic differentiation of mesenchymal stem cells derived from human adipose tissue by increasing TAZ expression. J. Cell. Physiol., 223, 168-177.
6. Cho, H.H., et al. (2010) NF-B activation stimulates osteogenic differentiation of mesenchymal stem cells derived from human adipose tissue by increasing TAZ expression. J. Cell. Physiol., 223, 168-177.
7. Cui, Q., et al. (2007) A map of human cancer signaling, Mol. Syst. Biol., 3, 152.
8. Deng, M., et al. (2003a) Prediction of protein function using protein-protein interaction data. J. Comput. Biol., 10, 947-960.
9. Deng, X., et al. (2003b) Mirk/dyrk1B is a Rho-induced kinase active in skeletal muscle differentiation. J. Biol. Chem., 278, 41347-41354.
10. Eisen, M.B., et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
11. Era, T. (2002) Bcr-Abl is a "molecular switch" for the decision for growth and differentiation in hematopoietic stem cells. Int. J. Hematol., 76, 35-43.
12. Gama-Castro, S., et al. (2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) . Nucleic Acids Res., 39, D98-D105.
13. Gibbons, F.D. and Roth, F.P. (2002) Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res., 12, 1574-1581.
14. Harris, S.E., et al. (2002) A model of transcriptional regulatory networks based on biases in the observed regulation rules. Complexity, 7, 23-40.
15. Herbst, R.S. (2004) Review of epidermal growth factor receptor biology. Int. J. Radiat. Oncol. Biol. Phys., 59, S21-S26.
16. Hishigaki, H., et al. (2001) Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast, 18, 523-531.
17. Itzhack, R., et al. (2013) Long loops of information flow in genetic networks highlight an inherent directionality. Syst. Biomed., 1, 35-34.
18. Karaoz, U., et al. (2004) Whole-genome annotation by using evidence integration in functional-linkage networks. Proc. Natl Acad. Sci. USA, 101, 2888-2893.
19. Kauffman, S. (1993) The Origins of Order: Self Organization and Selection in Evolution. Oxford University Press, New York, NY, USA.
20. Kauffman, S., et al. (2003) Random Boolean network models and the yeast transcriptional network. Proc. Natl Acad. Sci. USA, 100, 14796-14799.
21. Kauffman, S., et al. (2004) Genetic networks with canalyzing Boolean rules are always stable. Proc. Natl Acad. Sci. USA, 101, 17102-17107.
22. Klesse, L.J., et al. (1999) Nerve growth factor induces survival and differentiation through two distinct signaling cascades in PC12 cells. Oncogene, 18, 2055-2068.
23. Krause, D.S., et al. (2001) Multi-organ, multi-lineage engraftment by a single bone marrow-derived stem cell. Cell, 105, 369-377.
24. Lee, Y.S., et al. (1998) Differentiation of cultured human epidermal keratinocytes at high cell densities is mediated by endogenous activation of the protein kinase C signaling pathway. J. Invest. Dermatol., 111, 762-766.
25. Lin, T., et al. (2004) p53 induces differentiation of mouse embryonic stem cells by suppressing Nanog expression. Nat. Cell Biol., 7, 165-171.
26. Liou, H.C., et al. (1994) Sequential induction of NF-kappa B/Rel family proteins during B-cell terminal differentiation. Mol. Cell. Biol., 14, 5349-5359.
27. Martin, S., et al. (2007) Boolean dynamics of genetic regulatory networks inferred from microarray time series data. Bioinformatics, 23, 866-874.
28. Mori, C., et al. (1995) Programmed cell death in the interdigital tissue of the fetal mouse limb is apoptosis with DNA fragmentation. Anat. Rec., 242, 103-110.
29. Moustakas, A., et al. (2002) Mechanisms of TGF- signaling in regulation of cell growth and differentiation. Immunol. Lett., 82, 85-91.
30. Nelms, K., et al. (1999) The IL-4 receptor: signaling mechanisms and biologic functions. Annu. Rev. Immunol., 17, 701-738.
31. Okkenhaug, K. and Vanhaesebroeck, B. (2003) PI3K in lymphocyte development, differentiation and activation. Nat. Rev. Immunol., 3, 317-330.
32. Pang, L., et al. (1995) Inhibition of MAP kinase kinase blocks the differentiation of PC-12 cells induced by nerve growth factor. J. Biol. Chem., 270, 13585-13588.
33. Pittenger, M.F., et al. (1999) Multilineage potential of adult human mesenchymal stem cells. Science, 284, 143.
34. Rincon, M. and Pedraza-Alva, G. (2003) JNK and p38 MAP kinases in CD4 and CD8 T cells. Immunol. Rev., 192, 131-142.
35. Schwikowski, B., et al. (2000) A network of protein-protein interactions in yeast. Nat. Biotechnol., 18, 1257-1261.
36. Serra, R., et al. (2007) Why a simplemodel of genetic regulatory networks describes the distribution of avalanches in gene expression data. J. Theor. Biol., 246, 449-460.
37. Serra, R., et al. (2004) Genetic network models and statistical properties of gene expression data in knock-out experiments. J. Theor. Biol., 227, 149-157.
38. Sharan, R., et al. (2007) Network-based prediction of protein function. Mol. Syst. Biol., 3, 88.
39. 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.
40. Takahashi, K., et al. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 131, 861-872.
41. Takahashi, K. and Yamanaka, S. (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126, 663-676.
42. Vazquez, A., et al. (2003) Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol., 21, 697-700.
43. Zhou, X., et al. (2002) Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl Acad. Sci. USA, 99, 12783-12788.