|Posted on June 23, 2020 at 2:05 PM||comments (0)|
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:
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).
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.
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).
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
|Posted on February 20, 2020 at 9:25 AM||comments (0)|
Youwen received a SPARC award from the Office of the Vice President for Research to perform "Analyses of Transcriptomes Associated with Protein Quality Control in Endoplasmic Reticulum".
|Posted on November 18, 2019 at 9:25 AM||comments (0)|
Dear Peromyscus users,
Deer mice go West! Professors Anthony Long and Alan Barbour from the University of California at Irvine will be organizing a Peromyscus Symposium in Orange County, CA. The provisional dates have been set for June 17-20, 2020. This will be the 2nd Peromyscus Symposium following the first one in Columbia, SC in 2018, and the PGSC will be co-organizer of this significant event. We are very excited to see Tony and Alan undertaking this task and we are sure that it is going to be a huge success! This is again going to be an informal meeting bringing the Peromyscus community together!
For planning purposes we would appreciate contacting us about ideas, suggestions and your intention to attend, including number of participants from your team.
Our emails are:
|Posted on November 18, 2019 at 9:20 AM||comments (0)|
Congratulations to Amanda Havighorst for succesfully defending her PhD!
|Posted on May 4, 2019 at 2:25 PM||comments (0)|
The latest issue of the Newsletter of the Peromyscus Genetic Stock Center is out. You can read it here