scanMiRApp (original) (raw)

Select a miRNA collection

• Pre-built

• Custom sequence

• Transcript

Type in the first few letters of a gene name to populate the list

Selected miRNAs: (type in to filter)

The conservation status of miRNAs is obtained fromTargetScan

Minimum distance in NT between two binding sites of the same miRNA

Ribosomal shadow at the beginning of the 3'UTR, recommended is 15 NT

Maximum log_kd to report

Search also for non-canonical sites

Hover on points to view details, and click to visualize the alignment on the target sequence. You may also select miRNAs to show/hide by clicking on the legend.

Number of top miRNAs displayed

Double click on a row to visualize the alignment on the target sequence.

Download all

TargetScan conservation status

micro-RNAs (miRNAs) regulate transcripts stability and translation by targeting the Argonaute complex to RNAs exhibiting a partial complementarity with, in particular, the miRNA's seed sequence. For a general review on miRNA biology and targeting, seeBartel (2018).McGeary, Lin et al. (2019) have additionally shown the relevance of flanking nucleotides by empirically measuring the affinity (specifically the dissociation rate constant, KD) of a set of miRNAs to random 12-mer sequences, and then computationally extrapolating to other miRNAs). The scanMiR package, to which this app is an interface, builds on this work to offer a powerful and flexible binding and repression prediction framework.

For a quick tour of the app, click here.

There are two main ways to use scanMiRApp:

Transcript-centered:

In the 'Search in gene/sequence' menu, you'll be able to scan the sequence of a given transcript for binding sites of (sets of) miRNA(s).

miRNA-centered:

In the 'miRNA-based' tab on the left, you'll be able to visualize information relative to a selected miRNA, including for instance its general binding profile and its top targets.

The shiny app was developed by Pierre-Luc Germain and Michael Soutschek in the context of broader research in the Schratt lab.
Bugs reports and feature requests are welcome on the github repository.