What it does
QuanTP correlates transcript abundance and protein abundance to examine the association between them.
It either takes in the log fold-change of abundances as input or raw abundances from different conditions where it calculates the log ratios of abundances between two conditions.
Transcript input file can be generated from the quantitative RNA-Seq study whereas Protein input file can be generated from quantitative analysis of mass-spectrometry-based protein data.
Input file formats
Protein data file
First column - Gene
Following columns - Abundance values (or log fold-change values)
Example of Protein input file
Gene | sample1 | sample2 | sample3 | sample4 | sample5 | sample6 | sample7 | sample8 |
GeneX | value | value | value | value | value | value | value | value |
GeneY | value | value | value | value | value | value | value | value |
GeneZ | value | value | value | value | value | value | value | value |
Transcript data file
First column - Gene
Following columns - Abundance values (or log fold-change values)
Example of Transcript input file
Gene | sample1 | sample2 | sample3 | sample4 | sample5 | sample6 | sample7 | sample8 |
GeneX | value | value | value | value | value | value | value | value |
GeneY | value | value | value | value | value | value | value | value |
GeneZ | value | value | value | value | value | value | value | value |
Data input type
If data input type is abundance, experiment design file is required.
Example of experiment design file
case | groupA |
control | groupB |
sample1 | groupA |
sample2 | groupA |
sample3 | groupA |
sample4 | groupA |
sample5 | groupB |
sample6 | groupB |
sample7 | groupB |
sample8 | groupB |
Note: No title/header in experiment design file and the first two lines of the experiment design must have keyword "case" and "control"