Transcriptomic grading system in PDAC.

Reference transcriptomic technologies:

Identification of transcriptomic features:


Load data

Download example
Download output

Introduction

This application provide a molecular grading system based on transcriptome of PDAC.

User instructions

The user must provied one csv file:

  • The csv file with semi separated column and dots for decimals.
  • The csv file must contain a normalized expression matrix (The method was tested for data in log2 scale and upper-quatile normalized counts in case of RNA-seq ).
  • The matrix rows must contains the unique gene IDs or symbols. The samples ids must be in columns. The gene symbols should be in upper case.This file must be loaded in the Load data browser.

After loading the data, the user should select one of the four reference datasets to make prediction of the molecular gradient. The transcriptomic technology of user's data must be the same as the selected reference technology.

Try example:

If you want an example dataset to run our application, clic on the Download example button. The downloaded csv on your local disck contains the Affymetrix transcriptomic data of 6 samples from Puleo's cohort. You can load this example dataset in the browser Load Data after selecting the Puleo-microarrays reference transcriptomic technology and Gene IDs as identifier type of transcriptimc features.

Outputs:

The app wil provide two output. The first one is the table that reports the modcular gradient score of each sample in the panel Prediction. The favorable clinical outcomes are associated with high molecular gradient scores.

The other one is the figure shown in the panel Plot. The figure shows the density curve of the molecular gradient in the reference dataset. The predicted molecular gradient for each sample is represented by dots along the x axis of density curve.

Responsability:

This application was created for research purpose only. We decline any responsibility in case of use this application for clinical diagnostic or therapeutic purposes. This software comes with absolutely no warranty.