IIKmTA: Inter and Intra Kingdom miRNA Target Analyzer

Terminologies

miRNA: microRNAs (miRNAs) are a class of small, endogenous RNAs of 21-25 nucleotides (nts) in length. They play an important regulatory role in animals and plants by targeting specific mRNAs for degradation or translation repression.

Target: Specific mRNAs which are regulated by miRNAs.

E-cutoff: Expectation value is the penalty for the mismatches between small RNA mature and target sequence. Higher value indicated less similarity (and possibility) between small RNA and target candidate. The default penalty rule is set up by scoring schema. Maximum expectation is the cutoff; any small RNA-target pair with expecation less than the cutoff will be discarded in final result. The recommended values are 3.0-5.0 depending on scoring schema.

Intra-kingdom: When miRNA from one kingdom (eg., plant) is regulating the target gene of other kingdom (eg, plant).

Inter-kingdom: When miRNA from one kingdom (eg., plant) is regulating the target gene of the same kingdom (eg, animal).

To use the tool

Click the radio button to select Inter or Intra Kingdom
Select miRNA and Target from the drop down menu
Set the E-cutoff and click 'Submit'

The results will be displayed. At most 50 results will be shown on the screen. However the full set of results can be saved. One can navigate to the description of miRNA(s) and target(s) by clicking the respective link(s)

To save the full result click 'Download following result'.
Next two types of analysis can be performed:
1. miRNA → Target
2. Target → miRNA

To start miRNA to target analysis click 'miRNA → Target'. A appearence will change. The left box contains the list of miRNAs at user defined expectation value.

To analyze the miRNA(s) of interest the user must move the miRNA(s) from left box to'Selected miRNAs for analysis' box.

Select miRNA(s) of interest and click 'Move Right'. The user may use CTRL+Click or SHIFT+Click for multiple selection
To remove miRNA(s) from 'Selected miRNAs for analysis' box, select the miRNA(s) and click 'Move Left'
Here two types of analysis can be done
1. miRNA -> Target
2. miRNA pair -> Target set

To start miRNA to target analysis click 'miRNA → Target'. The results will appear below.

To save the results click 'Download following result'
To view the targets click '[+] View'

To perform the other type of analysis click 'miRNA pair → Target set'

To save the result click 'Download following result'
To view the targets click '[+] View'

Similarly Target to miRNA analysis can be performed by clicking 'Target → miRNA'.