Chapter 1 Introduction
1.1 Antibody Array Technologies and Applications
1.2 Protein Phosphorylation, Localization and Function
1.3 Interaction Proteomics and Pathway Building
1.3.1 BMP2 Signaling
1.3.2 The Effect of STI571 on Cell Signaling
Chapter 2 Technologies
2.1 Materials
2.1.1 Cell Lines
2.1.2 Chemicals
2.1.3 Antibodies
2.1.4 Protein-Molecular Weight Marker
2.1.5 Apparatus
2.2 Methods
2.2.1 Cell Culture
2.2.2 Cell Numbers and Experimental Format
2.2.3 Cytoplasmic and Nuclear Protein Extracts
2.2.4 Determination of Protein Concentration
2.2.5 Ponceau S Staining
2.2.6 Western Analysis
2.2.7 Immunoprecipitation
2.2.8 Cell Cycle Analysis
2.3 Silver Staining in ArrayTube
2.3.1 Biotinylation of Cellular Proteins
2.3.2 Incubation of Protein Extracts
2.3.3 Silver Staining
2.3.4 Statistical Analysis
Chapter 3 New Cytoplasmic and Nuclear BMP2-Signaling Pattern in U937 Cells
3.1 Modulation of Phosphorylation and Localization in BMP2-Treated U937 Cells
3.1.1 Total p-Tyrosine and p-p38, p38 Increased: Increasing Cytoplasm and Nucleus
3.1.2 Total p-ERK and p-JNK Increased: Increasing Cytoplasm and Unchanged Nucleus
3.1.3 Total p-Akt Increased: Increasing Cytoplasm and Decreasing Nucleus
3,1.4 Total p-Smadl, p-Smad2/3, c-Myc and p-STAT3 Unchanged:Decreasing Cytoplasm and Increasing Nucleus
3.1.5 Total p-p70S6 Unchanged: Increasing Cytoplasm and Decreasing Nucleus
3.2 BMP2 Signaling in U937 Cells
3.2.1 BMP2 Activates Akt, ERK and INK Pathway in U937 Cells
3.2.2 BMP2 Activates Smadl and Smad2/3 Networks, p38 Network and c-Myc, Tyrosine Network in U937 Cells
3.2.3 BMP2 Inhibits p70S6 Signaling in U937 cells
3.3 BMP2 Signaling Model in U937 Cells
Chapter 4 New Cytoplasmic and Nuclear BMP2-Signaling in MCF7 Cells
4.1 Modulation of Phosphorylation and Localization in BMP2-Treated MCF7 Cells
4.1.1 Total p-JNK, p-Smadl, p-Smad2/3, p-p38 and p38 Unchanged:Increasing Cytoplasm and Decreasing Nucleus
4.1.2 p-Tyrosinc, p-STAT3, p-ERK and p-p70S6 Increased:Increasing Cytoplasm and Unchanged Nucleus
4.1.3 Total c-Myc Unchanged: Slightly Increasing Nucleus and Slightly Decreasing Cytoplasm
4.1.4 Total p-Akt Unchanged: Unchanged Nucleus and Cytoplasm
4.2 BMP2 Signaling in MCF7 Cells
4.2.1 BMP2 Activates p70S6 and ERK Signaling, Tyrosine and STAT3 Network in MCF7 Cells ..
4.2.2 BMP2 Inhibits p38, JNK and Smad Signaling in MCF7 Cells
4.2.3 BMP2 Activates c-Myc Signaling in MCF7 Cells
4.3 BMP2 Signaling Model in MCF7 Cells
Chapter 5 New Cytoplasmic and Nuclear ST1571 Signaling in K562 Cells
5.1 Modulation of Phosphorylation and Localization in STI571-Treated K562 Cells
5.1.1 Total p-Akt and p-p70S6 Decreased: Decreasing Cytoplasm and Nucleus
5.1.2 Total p-p38, p38, c-Myc, p-Tyrosine, p-Smadl and p-Smad2/3 Increased: Increasing Cytoplasm and Nucleus
5.1.3 Total p-STAT3 and p-JNK Increased: Increasing Cytoplasm and Unchanged Nucleus
5.1.4 Total p-ERK Increased: Decreasing Cytoplasm and Increasing Nucleus
5.2 STI571 Signaling in K562 Cells
5.2.1 STI571 Inhibits Akt/p70S6 PI3K Signaling in K562 Cells
5.2.2 STI571 Activates p38 MAPK Pathway, c-Myc, Tyrosine and SmadI/Smad2/Smad3 Networks in K562 Cells
5.2.3 ST[571 Activates ERK Pathway in K562 Cells
5.2.4 ST1571 Activates STAT3 Network and JNK/MAPK Pathway in K562 Cells
5.3 STI571 Signaling Model in K562 Cells
Chapter 6 Positive and Negative Co-localized Relationships in Three Treated Cell Lines
6.1 Positive and Negative Co-localized Distributions
6.1.1 p-p38 and p38
6.1.2 Smadl and Smad2/3
6.1.3 Akt, ERK and p70S6
6.1.4 p70S6 with p38 and Smad1, 2, 3
6.1.5 ERKor p38 with Smadl
6.1.6 ERK or p38 with c-Myc
6.2 Possible Relationships
Chapter 7 Cytoplasmic Signaling in Three Treated Cell Lines
7.1 Cytoplasmic Distribution
7.1.1 p-ERK, p-JNK and p-Akt in BMP2-Induced Apoptosis in U937 Cells
7.1.2 p-STAT3 and p-JNK in STI571-Treated K562 Cells
7.1.3 p-Tyrosine, p-STAT3, p-ERK and p-p70S6 in BMP2-Treated MCF7 Cells
7.2 Co-cytoplasmic Signaling
Chapter 8 Proteomic Silencing in Treated Human Cancer Cell Lines
8.1 Proteomic Silence Distributions
8.1.1 p-p70S6 Nuclear Decrease in BMP2-Induced Apoptosis in U937 Cells
8.1.2 p-ERK/p-JNK/p-p38, p-Smadl and p-Smad2/3 Co-nuclear Decrease in BMP2-Treated MCF7 Cells
8.1.3 p-Akt and p-p70S6 Co-cytoplasmic and Co-nuclear Decrease in STI571-Treated K562 Cells
8.2 Possible Relationships
Chapter 9 Signaling Pathway Setting-up Based on Bioinformatics
9.1 Methods
9.1.1 Mean and Variance
9.1.2 Hierarchical Clustering
9.1.3 Competitive Learning Network
9.1.4 Self-Organizing Map (SOM)
9.2 Results
9.2.1 Mean and Variance Analysis of Cytoplasmic Signaling in Control and STI571-Treated K562 cells
9.2.2 Competitive Learning Network Analysis of Cytoplasmic Signaling in Control and STI571-Treated K562 cells
9.2.3 Hierarchical Clustering Analysis of Cytoplasmic Signaling in Control and STI571-Treated K562 cells
9.2.4 SOM Analysis of Cytoplasmic Signaling in Control and STI571-Treated K562 cells
9.3 Discussion
9.4 Conclusions
References
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