Navigation & FAQ

Network reconstruction

• Step 0: Preparations
• Step 1: Load gene expression datasets for network reconstruction (exp-load)
  • Q&A: The choice of expression dataset for network reconstruction
  • Q&A: Input RNA-Seq dataset
  • Q&A: Input expression matrix not from the GEO database
• Step 2: Normalization for the expression dataset (exp-QC)
  • Q&A: QC for an RNA-Seq dataset
  • Q&A: Combining two datasets
• Step 3: Check sample cluster information (optional) (exp-cluster)
• Step 4: Prepare files to run SJARACNe (sjaracne-prep)
  • Q&A: ID conversion

Driver inference

• Step 0: Preparations
• Step 1: Load the expression dataset for analysis (exp-load, exp-cluster, exp-QC)
  • Q&A: What to do if the ID types from network-reconstruction dataset and analysis dataset are different?
• Step 2: Read in network files and calculate driver activity (act-get)
  • Q&A: Why study driver’s activity ?
• Step 3: Obtain differential expression (DE) / differential activity (DA) for drivers (act-DA)
• Step 4: Generate a master table for drivers (ms-tab)
  • Q&A: How to interpret and use the master table

Advanced analysis

• Preparations
• Part I: More details about the top drivers
  • QI.1: How do I obtain the top drivers with significant differential activity (DA) in the comparison of G4 MB vs. other subtypes ?
  • QI.2: How do I interpret the significance of the top DA drivers ?
  • QI.3: What is the expression/activity pattern of these top DA drivers across sample subtypes?
  • QI.4: What are the biological functions of these top DA drivers ?
  • QI.5: What are the biological functions of the target genes of these top DA drivers ?
• Part II: More details about the selected driver
  • QII.1: How do I interpret the significance of the selected driver ?
  • QII.2: How do I visualize the network structure of the selected driver ?
  • QII.3: What is the expression/activity of this selected driver across samples of different subtypes ?
  • QII.4: What are the functions of the target genes of this selected driver ?
• Part III: Other analyses that NetBID2 can perform
  • QIII.1: What are the activities of the curated gene sets across all samples ?
  • QIII.2: How do I determine whether drivers share significantly overlapping target genes ?
  • QIII.3: How do I draw oncoPrint figures for samples with different mutation information ?
    • Q&A: How to modify the figure size created by draw. functions ?