Release 1.2, Mar 19, 2013
Contact: Jin Gu, wellgoo@gmail.com
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1. Input file
   1) The miRNA target genes with context scores from TargetScan
     ./miRNA/TS6.2-hsa.miRFam-GeneID.cons1.txt
   2) The gene expression profile of the differentially expressed genes
     ./example/gse19804.top10k.ttest-BH.logfc.txt
   3) The list of the studied genes
     ./example/gse19804.top10k.gene.txt
     
2. Generate the miRNA target gene set and the control miRNA target gene sets
  script:
    miR-TS-rand.pl
    miR-TS-rand.md5.pl (an advanced method is used to generate the random numbers)
  command:
    perl miR-TS-rand.pl [the study gene list] [TargetScan file] -1 > [miRNA_target_gene_set]
    perl miR-TS-rand.pl [the study gene list] [TargetScan file] [the number of permutation] > [control_gene_set]
  example:
    perl miR-TS-rand.pl ./example/gse19804.top10k.gene.txt ./miRNA/TS6.2-hsa.miRFam-GeneID.cons1.txt -1 > TS6.2-Geneset-Cons1.luc-gse19804.txt
    perl miR-TS-rand.pl ./example/gse19804.top10k.gene.txt ./miRNA/TS6.2-hsa.miRFam-GeneID.cons1.txt 10000 > TS6.2-Geneset-Cons1-Ctrl10k.luc-gse19804.txt
      [NOTE: it will take a long time and large disk space to generate the control miRNA gene set.]

3. Establish the hierarchical gene co-expression signatures of the differentially expressed genes
  script:
    clustering.pl (it will use other scripts to finish the clustering)
  command:
    perl clustering.pl [gene_expression_matrix] [cutoff] [min_cluster] [cluster file]
      gene_expression_matrix: the expression values of studied genes
      cutoff: the cutoff for cutting the gene co-expression hierarchy (default: "spearman_zscore:0.52")
      min_cluster: the minimum size of the gene co-expression signature (default: 10% of the number of input genes; in the example dataset, 3699 differentially expressed genes were studied, so it is set as 370~=3699*0.1)
  example:
    perl clustering.pl ./example/gse19804.top10k.ttest-BH.logfc.txt spearman_zscore:0.52 370 gse19804.cluster-size010.luc-normal.ttest-BH.miRHiC.r10k.txt

4. The main program of miRHiC
  script:
    miR-HiC.pl
  command:
    perl miR-HiC.pl [miRNA_target_gene_set] [control_gene_set] [cluster_file] > [miRHiC result]
      miRNA_target_gene_set: generated by miR-TS-rand.pl (refer to Section 2)
      control_gene_set: generated by miR-TS-rand.pl (refer to Section 2)
      cluster_file: generated by clustering.pl (refer to Section 3)
  example:
    perl miR-HiC.pl TS6.2-Geneset-Cons1.luc-gse19804.txt TS6.2-Geneset-Cons1-Ctrl10k.luc-gse19804.txt gse19804.cluster-size010.luc-normal.ttest-BH.miRHiC.r10k.txt > result.miRHiC.txt