Usage Instructions

Step 1: Select an organism

Select one of the following organisms supported by miTEA:

• Caenorhabditis elegans
• Drosophila melanogaster
• Danio rerio (Zebrafish)
• Homo sapiens
• Mus musculus
• Rattus norvegicus

Step 2: Paste a ranked list of gene/protein names

Paste here a list of gene (or protein) names. For example:

CHMP5

RAB6C

ZNF394

FAM3B

NM_003174

etc...

Remarks:

* Each line should contain one gene name.

* The preferred format is gene symbol. Other supported formats are: gene and protein RefSeq, Uniprot, Unigene and Ensembl. Use WebGestalt for conversion from other identifier formats.

* Notice that the processed list of genes may contain less genes than in the input list. This is because not all genes are scored or considered by the relevant target prediction tool.

Step 3: Select a miRNA target prediction tool

 Select one of the following miRNA target prediction tool:

1. TargetScan

2. MicroCosm

3. EiMMo

Parameters

P-value threshold - Only miRNAs for which we find target enrichment with a p-value better than this threshold are reported.

Note that this p-value does not include the multiple hypothesis correction on the number of miRNAs tested. To correct for this (Bonferroni multiple testing correction) the p-value should be multiplied by the number of miRNAs used as reported in the results page.

Output results in Microsoft Excel format - If checked, an Excel file with the results will also be generated.

Output unresolved and duplicate genes - If checked, additional files with the lists of all genes miTEA did not recognize and genes which appeared in the list more than once will be generated.

Run miTEA in fast mode - If checked then miTEA will only attempt to put the threshold separating between the target set and the background set in the top 10% of your list (or, at least 1,000 genes).

Output

The output of the software consists of a color-coded trimmed graph of all significantly enriched miRNA targets.  Clicking on a node in the color-coded graph will show the enrichment p-value, the genes targeted by the miRNA that are also located in the top of the input list and a link to more information on this miRNA. 

Output example: