ComiR: Combinatorial miRNA
target prediction tool

miRNA Input
Select species:
Select the species of interest.
The miRNA target prediction will be restricted on the 3\'UTR sequences collected for the selected species.
You can include in the analysis your custom mRNA sequences by using the dedicated panel below.
For more info click on ?

Input a set of miRNAs
one set: it contains the 28 Drosophila miRNAs (with abundance levels) used to train ComiR.
many sets: it contains the abundance levels of 974 human miRNAs in 4 conditions (click ? for more info). This example automatically enables the selection of the top expressed miRNA avaliable in the Advanced search panel.
Input the list of miRNAs. The following formats are accepted:
1)list of miRNAs
hsa-let-7a-5p
hsa-miR-1-5p
hsa-miR-130a
...
2)table of miRNA abundances (header line required, comma separated fields)
miRNA,cond1,cond2,cond3
hsa-let-7a-5p,3240,230,55
hsa-miR-1-5p,33,890,4570
hsa-miR-130a,550,630,290
...
miRNA ids will be converted to the latest mirBASE notation.
Two examples are provided.
Load miRNAs from file:
Data is in log-scale
Check the box if data is in log-scale (i.e. microarray data). Don't check the box if data is in linear-scale (i.e. miRNA-seq reads). If you check the box, data will be exponentialized before computing the concentrations.

mRNA custom sequences Input (optional)

Input mRNAs
Input the mRNA custom sequence(s) to be included in the target prediction analysis.
FASTA format only.


Load mRNAs from file:

More Options

Treat the input list of miRNAs as a set or as single miRNAs

Compute p-value
H.sapiens species only
If you enable this option, ComiR will associate to each putative target a p-value based on scrambled sequences targeting predictions.

miRNA list filtering
Use the top expressed miRNAs covering % of total miRNA abundance
If your miRNA input contains information about the miRNA abundance, this option will remove from the analysis all the lowly expressed miRNAs. Specifically, for each set of miRNA abundances, only the top expressed miRNAs whose sum reaches the selected percentage of the total miRNA abundance will be used.
Use the top expressed miRNAs with an expression level higher than
If your miRNA input contains information about the miRNA abundance, this option will remove from the analysis all the lowly expressed miRNAs. Specifically, for each set of miRNA abundances, only the top expressed miRNAs whose expression level is higher than the input value will be used.
Load the list of miRNAs to be excluded from the filtering from file:
If you chose to filter your input miRNA list using the two options above, you can exclude from the filtering a list of miRNAs, which will be included in the analysis even if they don't pass the expression level based filtering. For instance, this option can be used to input the list of differentially expressed miRNAs and be able to predict the targets of the top expressed together with the differentially expressed miRNAs.




Technical problems? Comments/suggestions? Please email clc196(AT)pitt.edu

       

  Supported by the National Library of Medicine - NIH
  Fondazione RiMED

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