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File Format

File format should be, e.g.,
gene    groupA.1    groupA.2    groupB.1    groupB.2
NM_001654    0.134    0.225    1.334    2.333
....
i.e., in the first row, the first column should be the word "gene". Then comes names of two groups of samples. Each is as the form of XXX.N, where XXX is the group name and N is integer starting from 1. Rows below includes gene ID, and gene expression. Here is an example. User can upload file directly or paste.

Options

• Species: name of species for which gene expression is measured.
• Conservation of miRNAs : based upon TargetScan Release 6.0
• Gene identifier: type of identifier of genes

RefSeq mRNA id  is primary one. Any others are converted from it via BioMart.

• Type of treatment of samples:

Gene expression is transfered to log-transformed ratio between individual sample within each group. For the case of example, there are four combinations, log(neg.1/day1.1), log(neg.2/day1.1), log(neg.1/day1.2), log(neg.2/day1.2). Then

• mean : simple mean
• mixed : as it is
• one by one : each of combinations is analyzed independently


• Method: statistical method to compute P-values
• t.test : Parametric test, sensitive to difference of average
• Wilcox test : Non-parametric test, sensitive to difference of average
• Kolmogorov Smirnov test : recommended. Non-parametric test, sensitive to difference of both average and variance.
  

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