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Table 1 Case studies summary

From: Visualizing Meta-Features in Proteomic Maps

  CASE STUDY 1 CASE STUDY 2 CASE STUDY 3
DESCRIPTION Involves the proteins participation in interaction networks and pathways. Combines the differentially expressed proteins with basic meta-features (e.g., protein type, protein location, mol. function) Associates the proteins with discovered post-translational modifications (PTMs)
QUESTIONS
ADDRESSED
Q1: Which are the up/down regulated proteins that participate in the network N? Q1: Which proteins were found to be differentially expressed based in both the X and Y iTRAQ ratios? Q1: Are the phosphorylated proteins also differentially expressed?
  Q2: What are the molecular functions of the proteins that belong to network N? Q2: Are there any upregulated proteins found only in the X or in the Y iTRAQ ratio? Q2: Which proteins have undergone phosphorylation?
  Q3: What types of proteins (e.g., enzymes, transporters) are involved in the network N? Q3: What is the location of the differentially expressed proteins? Q3: What is the peptide sequence that is "responsible" for a phosphorylated protein?
  Q4: What types of proteins appear in pathway P? Q4: What types of proteins (e.g., enzymes, transporters) are up-regulated? Q4: Do the proteins that have undergone oxidation belong to any network/pathway?
  Q5: Which molecular functions/biological processes are assigned to the proteins that belong to pathway P? Q5: What are the molecular functions/biological processes associated with the up-regulated proteins? Q5: What is the function of the proteins that have undergone acetylation?
  Q6: Are there any common proteins in pathways P1 and P2?   
PFMs
USED
Network Map PFM=[belongs to network N, fold change] Differential Expression Comparison Map PFM=[iTRAQ ratios comparison state, iTRAQ differential expression] Phosphorylation Map PFM=[has undergone phosphorylation, iTRAQ ratio]
  Pathway Map PFM=[belongs to pathway P, protein type]   
  1. A summary of the scenarios presented and discussed in the paper: short description, real-life questions concerning each scenario and the corresponding PFMs. The notation PFM = [feature1, feature2] is used to show quickly the two features that have been associated with the size and color of the spheres respectively.