microRNA and RNA binding protein Interaction statistic measures

Download for Pumilio (PUM)

Download for UAUUUAU (AU-rich element)

Two types of microRNA recognition seeds (m8 and 1A) are processed separately. Definition of header columns are listed below:

Methods of microRNA identity randomization:
chrom The microRNA binding site identities are randomized across the same chromosome.
AU The microRNA recognition seeds are classified the their AU-content (high, mid, low). Only microRNA binding sites within the same AU content category can swap their identities in the randomization.
decile The microRNA binding sites are classified by their relative position on the 3'UTRs ("0" on the beginning to "9" on the end). Only microRNA binding sites with the same 3'UTR relative position can swap their identities in the randomization.

Statistic values from microRNA identity randomization:
Real The number of neighboring binding sites within 50nts between each pair of microRNA and RNA binding protein.
Random The expected number of neighboring binding sites calculated from the average of 10000 shuffles.
Std The standard deviation of numbers of neighboring binding sites from 10000 shuffles.
Zscore (Real-Random)/Std
Ratio Real/Random
Pvalue Empirical Pvalue calcuated as the fraction of random neighboring binding site counts that are greater than or equal to the real number of neighboring binding sites.

For the details, please read our publication:
Computational assessment of the cooperativity between RNA binding proteins and microRNAs in transcript decay

The source code used in miRNA RBP recognition motif colocalization analysis is release as CCAT package.

For technical support, please email