Subtype analysis with Pathway Logic (PL-Subtype)
Visit Github repository of PL-Subtype and follow the instruction in README.
To run PL-Subtype, You need 1) two input files (see Input Files below) and 2) pathway(s) of interest.
1. If you have your pathway(s) of interest, see Case1 in README.
2. If you would like to analyze on recommended pathways from DEG analysis, see Case2 in README.
Two result files (see Result Files below) will be generated and used for final step of subtype analysis with Pathway Logic Assistant (PLA) Online (GUI version of PLA).
Install JDK and download PLA Online, and proceed analysis with result files (see Subtype Analysis below).
Input files 1. Gene expression file
Gene expression file should be tab-delimited.
Example:
|
Sample1 |
Sample2 |
... |
SampleN |
| Gene1 |
8 |
11 |
... |
19 |
| ... |
19 |
21 |
... |
11 |
| Gene2 |
14 |
20 |
... |
10 |
2. Sample information file
Sample information file should be tab-delimited.
First column: Sample name, second column: subtype name
| Sample1 |
Normal |
| Sample2 |
Normal |
| ... |
... |
| SampleN-1 |
Basal |
| SampleN |
Basal |
Result files
| 1. DEGs_Normal-[subtype]_in_[pathway].txt |
DEG analysis is performed by Limma comparing Normal vs. each subtype. This file includes the list of DEGs in the user-selected pathway(s). |
| 2. Subtype-specific_TFs_in_[pathway].txt |
For each TF in user-selected pathway, TF analysis is performed using hypergeometric test to find whether the target genes of TF enrich in subtype DEGs. This file includes the hypergeometric test result of each TF. |