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Support #100

Time seres analysis

Added by Jon Ambler over 5 years ago. Updated over 5 years ago.

Status:
Resolved
Priority:
High
Assignee:
Jon Ambler
Start date:
10/04/2019
Due date:
% Done:

100%

Estimated time:
Spent time:
40.00 h

Description

Looking at the time series data for the samples, we needed to compare the expression of the different conditions (FKN, Scar, Keloid) to skin at time points do, d14, d28.

History

#1

Updated by Jon Ambler over 5 years ago

  • Status changed from New to In Progress
  • % Done changed from 0 to 30

Time series analysis was done using deseq2, and saved as an R script.

Exported the results to csv files

#2

Updated by Jon Ambler over 5 years ago

  • Status changed from In Progress to Resolved
  • % Done changed from 30 to 100

A python script to profile the time series data was created.

This script takes in the expression info from the different time points and determines if they show significant changes in direction.

For example:
d0: up, d14, up, d28 no change.

These were used to create profiles that grouped genes by similar expression patterns and times.

GSEA of these sets showed that the sets had distinct pathways.

Results exported and sent to Relebohile.

Also available in: Atom PDF