MMIA : microRNA and mRNA Integrated Analysis

 

    Overview  |   MMIA   |   Documentation 

Notice. Users should go through each step and then run the program.
Minimum requirements are to upload both miRNA expression data (or miRNA list) in step 1 and mRNA expression data in step 3.
(Recent changes)

 
MMIA workflow
Organism
 

  

 
Step 1. microRNA data analysis
 
A. Data section
  a. Regulated microRNA list (Example list)
  
  b. microRNA expression data    (Example file)   *Help
B. Option section  *Help
  a. Common options in the section A.
     The listed microRNAs or the microRNAs in group 2 are
      down-regulated. up-regulated.
  b. Options for the section A (b).
      Preprocessing options
         threshold ceiling floor
         filtering max_value/min_value max_value-min_value
         log2 transform
          standardization
         biclustering
      Test options
         fold-change of
         t-test with p-value
         fold-change of and t-test with p-value
      Multiple correction option(subjected to the second test)
         q-value :
 
Step 2. microRNA target algorithms
  1. You can select one of the target algorithms.  *Help

    • Make sure that "Skipped" is checked when you select two target algorithm intersection in option 2.
  2. Or you can use common target genes by intersection
    between your two selected target algorithms.
    • Algorithm 1    AND    Algorithm 2   
 
Step 3. mRNA data analysis
 
A. Data section   *Help
  mRNA expression data  Chip platform   (Example file, HG_U133Plus2)
B. Option section *Help
  Preprocessing options
      threshold ceiling floor
      filtering max_value/min_value max_value-min_value
      log2 transform
       standardization
  Test options
      fold-change of
      t-test with p-value
      fold-change of and t-test with p-value
  multiple correction  (subjected to the second test)
      q-value :
 
Step 4. miRNA and mRNA combined analysis
Method description
  1. KEGG  
  2. MIT MSigDB v2.5
  3. Disease
    • G2D (candidate genes to inherited diseases)
 
Step 5. Optional analysis
 
A. microRNA gene set analysis *Help
  1. Transcription factor binding sites enriched in promoter regions of miRNAs
  2. Diseases enriched in the microRNAs by using miR2Disease database
 B. miRNA and mRNA combined analysis by MIT GSEA software (will take 10 or more minutes) *Help
  1. MIT MSigDB v2.5