Kiaris Lab

Lab news

PhETA platform

Posted on June 23, 2020 at 2:05 PM

Dear colleagues,

 

We have developed PHeTA (https://ifestos.cse.sc.edu/PHTA_Calculator/) an online platform that performs Pearson correlation analyses and generates scatterplots of RNA seq (and other) data.

 

Some "real life" examples are the following:

 

Example 1

 

You want to generate a list of genes that correlate in expression with a given transcript and sort them accordingly (according to their degree of correlation).

 

Example 2

 

You want to test if the transcriptome that is co-regulated with gene A, correlates with a transcriptome that is co-regulated with gene B. You can also make scatter plots of Pearson’s correlations of A vs B.

 

Example 3

 

You have obtained RNAseq data from a set of specimens, and a list of phenotypic measurement for each one of these specimens (cell proliferation, height, sensitivity to COVID, ...anything). You want to identify which genes correlate, and at which extent, to the phenotype of interest.

 

 

 

A typical outcome (product) is a graph like this below that tells you that in this particular set of specimens, IL6 is inversely correlated with hspa5 (BiP).

 

 

image001.png

 

 

 

As you might have thought already, this was triggered by Peromyscus-related needs but it can be applied to any set of data.

 

The credits for the implementation of this project should go to Naga Venkata (JJ) Satti and Youwen Zhang, students at the College of Engineering and College of Pharmacy respectively, and Casey Cole, Instructor at the College of Engineering.

This is an ongoing project, with obviously, a lot of space for improvement. In the meanwhile we hope that it will be of use to you and we are looking forward to you feedback on “glitches”, user friendliness, and ideas for improvement.

 

 

Homay and Hippokratis

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