NanoString-Splice

About  |  Batch analysis  |  Custom dose-response curve analysis 

What is NanoString-Splice?:
NanoString-Splice is a web service to analyze the NanoString data for pre-mRNA splicing. It considers the potential impact of different hybridization efficiency of the two probes used in two splice isoforms and uses an optimization method to adjust the percent-splice-in (PSI) values. It also provides functions for drug dose-response analysis.

Download the source code:
NanoString-Splice is written in R. Download: NanoString-Splice-R-package.zip. Manual: NanoString-Splice_manual.pdf.

How to fill out the web-form?
There are two forms available. one for large amount of input data (batch analysis). It was designed for "single compound, multiple targets" analysis. It deals with normalized NanoString counts data for I- and S- probes and calculates Ei-adjusted PSI values and then do dose-response analysis.  Dose-response curves will be generated for each individual target in seperated plot. Another form (Custom dose-response curve analysis) is designed for "multiple compounds, single target" analysis. Only one plot (figure) will be generated with all compound-responses shown in different colors. The webforms are self-explanatory and click the "example" links to see examples. 

What are I- and S-probes?


I- and S-probes are two NanoString probe sets targeting the inclusion (I) and skipping (S) isoforms of an alternative exon.

What is Ei-adjusted-PSI?
"Ei" represents the relative hybridization efficiency of I-probe over S-probe. NanoString-Splice uses the R function “optimize” to find the Ei which minimizes the coefficient of variation (CV) of the total adjusted counts T=I/Ei+S ( I and S are the normalized counts for I- and S- probe respectively) for multiple samples.

Can I use NanoString-Splice to analyze other types of data?
Yes! The tool is optimized for NanoString data to study RNA splicing. However, it is designed to be flexible. Functions like Ei-adjustion, PSI calculation can be "turned off". Users can provide their own data (including counts data or percentage data) for dose-response analysis. Many parameters can be changed before running the tool (eg. Ec5x, Ec_PSI30 values can be calculated). It's also possible to study non-dose-response data. For example, one can calculate the Ei-adjusted-PSIs to study splicing changes in cells with certain factor knockdown. 

How to interpret the output data?
See this file for details.

Having questions and/or suggestions? Contact:
Dr. Li
PTC Therapeutics, Inc.
Email: wli@ptcbio.com